+

US20160326589A1 - Method of diagnosing patients with conditions caused by mendelian mutation - Google Patents

Method of diagnosing patients with conditions caused by mendelian mutation Download PDF

Info

Publication number
US20160326589A1
US20160326589A1 US15/146,867 US201615146867A US2016326589A1 US 20160326589 A1 US20160326589 A1 US 20160326589A1 US 201615146867 A US201615146867 A US 201615146867A US 2016326589 A1 US2016326589 A1 US 2016326589A1
Authority
US
United States
Prior art keywords
chr2
panel
chr1
genetic marker
proclivity
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Abandoned
Application number
US15/146,867
Inventor
Sultan Turki Al-Sedairy
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Individual
Original Assignee
Individual
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Individual filed Critical Individual
Priority to US15/146,867 priority Critical patent/US20160326589A1/en
Priority to PCT/US2016/030860 priority patent/WO2016179331A1/en
Priority to PCT/US2016/036953 priority patent/WO2016201272A1/en
Publication of US20160326589A1 publication Critical patent/US20160326589A1/en
Abandoned legal-status Critical Current

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • the present invention relates to genetic detection of conditions, and particularly to a method for diagnosing patients with conditions caused by Mendelian mutations, or diagnosing such patients as having a proclivity towards developing such conditions.
  • Genomics have ushered in a new era for clinical medicine.
  • the ability to scan the entire genome (or its coding part) for disease causing mutations relatively free of clinical bias has uncovered the limited sensitivity and specificity of making diagnoses on clinical grounds only. This was first apparent with the advent of array-CGH that specifically targets large genomic mutations. Subsequently, whole genome sequencing (WGS) and whole exome sequencing (WES) confirmed the same pattern. This raises the interesting question of whether all patients with a suspected genetic diagnosis should have WGS/WES as the initial diagnostic test. Pending data on the validity of this approach, one has to consider some practical challenges. Cost remains a significant hurdle that prevents most patients, especially in less wealthy countries, from accessing WGS/WES.
  • the method of diagnosing patients with conditions caused by Mendelian mutations is a genetic panel-based diagnostic method for determining if a patient has a condition (or a proclivity for a condition) based on detection of one or more specific genetic markers.
  • a sample is first obtained from a patient and the sample is assayed to determine the presence of at least one genetic marker.
  • the assay is a sequencing-based multiplexing assay designed for the detection of specific Mendelian mutations (the set of which are referred to herein as the “Mendeliome”).
  • the patient is then diagnosed with a particular condition (or with a proclivity for that condition) if the at least one genetic marker is detected.
  • the at least one genetic marker is selected from the group consisting of TTR, MYPN, TTN, COL4A3, KCNH2, SMAD4, NOTCH1, ANK2, PKP2, LDB3, MYH6, MYBPC3, SCN5A, MYL3, CACNA1C, DMD, BAG3, EHMT1, DSG2, ABCC9, KCNE2, RYR2, TTN, TTN-AS1, VCL, SOS1, ANKRD1, ACTN2, DSP, FBN1, CHD7 and combinations thereof.
  • the at least one genetic marker is selected from the group consisting of UBIAD1, LARS2, GJB2, HGF, MYO6, PCDH15, TMC1, MARVELD2, CDH23, OTOF, LRTOMT, LOXHD1, EDN3, MYO15A, SLC26A4, CLDN14, MARVELD2, WFS1, POU4F3, PTPRQ, SCARF2, COL4A4, USH2A, MYO7A and combinations thereof.
  • the at least one genetic marker is selected from the group consisting of XPC, COL7A1, ALDH3A2, SLC39A4, CTSC, ITGB4, TGM1, HPS1, TYR, LAMB3, EOGT, DOCK6, LAMC2, GORAB, KRT5, KRT83, COL18A1, ALDH18A1, FERMT1, EOGT, DCAF17, DSP, NF1 and combinations thereof.
  • the at least one genetic marker is selected from the group consisting of LIFR, TCOF1, LARP7, EVC, POC1A, HGSNAT, COL2A1, CRTAP, COL11A2, DYM, COL1A1, CREBBP, COL11A1, PYCR1, NIPBL, ROR2, EXT1, ACTB, ADAMTSL2, NEK1, DYNC2H1, IRF6, NSD1, UBE3B, DLL3, EP300, SGSH, EZH2, CHRNG, GALNS, MGAT2, TNFRSF11B, LMNA, ERCC8, CANT1, MMP2, FKBP10, CUL7, GNPAT, FGFR2, FGFR3, MASP1, FREM1, HSPG2, MEOX1, OBSL1, WNT1, COL1A2, COL1A1, ANTXR2, PEX13, ECEL1, KMT2A
  • the at least one genetic marker is selected from the group consisting of TBCE, GHR, GHRHR, BBS5, SHOX and combinations thereof.
  • the at least one genetic marker is selected from the group consisting of UGT1A1, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9, JAG1, BAAT, ATP7B, TJP2, EPCAM, ABCB4, ABCC2, LRBA, SLC10A2, ABCB11, VIPAS39, FAH, G6PC and combinations thereof.
  • the at least one genetic marker is selected from the group consisting of BLM, FANCA, FANCM, BRCA2, ASXL1 and combinations thereof.
  • the at least one genetic marker is selected from the group consisting of L2HGDH, MCCC2, SLC37A4, ARSB, HSD3B7, DBT, PHKG2, BTD, MUT, ASL, DPAGT1, ASAH1, AMT, BCKDHB, BCKDHA, CBS, PAH, CLN8, GBA, ACADM, SLC3A1, MMACHC, PTS, GNS, GCDH, SLC22A5, GAA, MMADHC, PYGL, ASS1, CPS1, H6PD, PTS, PGM1, IVD, ARG1, ASAH1, GLB1, OXCT1, OPLAH, FAH, G6PC, PEX1 and combinations thereof.
  • the at least one genetic marker is selected from the group consisting of L1CAM, ABCD1, DYSF, GBA2, TRAPPC9, CYP2U1, PANK2, ARL13B, KIF7, ERLIN2, PSAP, VAPB, FKTN, PLP1, GDAP1, ASPM, LAMA2, MECP2, CDK5RAP2, WDR81, ABAT, NDE1, WDR45B, H5D17B4, HEXA, SPG11, PDGFRB, HUWE1, SLC25A19, ARHGEF6, ADRA2B, RELN, CENPJ, ARL14EP, PHGDH, ARID1B, WNK1, SEPN1, RNASEH2C, RNASEH2B, CYP27A1, ATN1, AHI1, STXBP1, CDKL5, MED23, ISPD, CEP57, AGRN, FKRP, ADCK3, SCN2A, MFSD8, TYMP, FLV
  • the at least one genetic marker is selected from the group consisting of IL7R, JAK3, CD40LG, AK2, DCLRE1C, CD40, AICDA, MLPH, NHEJ1, RAB27A, RAG2, RAG1, BTK, ATM, LYST, CYBB, AIRE, DOCK8, SLC17A5, STATS, WAS, CD247, DNMT3B, FLG, NCF2, ADA, RFXANK, PTPRC, COLEC11 and combinations thereof.
  • the at least one genetic marker is selected from the group consisting of SFTPB, CFTR and combinations thereof.
  • the at least one genetic marker is selected from the group consisting of IQCB1, COL4A6, NPHP3, SLC4A4, DDX39A, SMARCAL1, PKHD1, LAMB2, NEK8, NPHP4, FRAS1, XDH, MKS1, FAN1, TCTN2, NPHS1, CC2D2A, TMEM231, UPK3A, CEP290, NPHP4, COL4A4, TMEM67, C5orf42, TMEM237 and combinations thereof.
  • the at least one genetic marker is selected from the group consisting of ALMS1, CRB1, CHST6, CRYBA1, PRSS56, GUCY2D, SNRNP200, PDE6C, CNGA3, C8orf37, ABCA4, BBS10, CERKL, GPR125, NHS, LTBP2, GCNT2, RLBP1, MIP, RP1L1, CHM, EYS, TULP1, IGFBP7, CYP1B1, LRAT, MERTK, CNNM4, RP1, RP2, LCA5, MFRP, CNGB1, CACNA1F, KCNV2, CRX, PROM1, TRPM1, PAX6, IMPG2, CDHR1, GPR179, CRYGC, CRYGD, NMNAT1, GALT, ARL6, LRP5, WDR19, SLC4A11, GDF3, SLC16A12, RGS9, RDH12, ADAMS, AIPL1, FAM161A, RPG
  • the method of diagnosing patients with conditions caused by Mendelian mutations is a genetic panel-based diagnostic method for determining if a patient has a condition (or a proclivity for a condition) based on detection of one or more specific genetic markers.
  • a sample is first obtained from a patient and the sample is assayed to determine the presence of at least one genetic marker.
  • the assay is a sequencing-based multiplexing assay designed for the detection of specific Mendelian mutations (the set of which are referred to herein as the “Mendeliome”).
  • the patient is then diagnosed with a particular condition (or with a proclivity for that condition) if the at least one genetic marker is detected.
  • the at least one genetic marker is selected from the group consisting of TTR, MYPN, TTN, COL4A3, KCNH2, SMAD4, NOTCH1, ANK2, PKP2, LDB3, MYH6, MYBPC3, SCN5A, MYL3, CACNA1C, DMD, BAG3, EHMT1, DSG2, ABCC9, KCNE2, RYR2, TTN, TTN-AS1, VCL, SOS1, ANKRD1, ACTN2, DSP, FBN1, CHD7 and combinations thereof.
  • the details of the cardiovascular panel are given below in Table 1.
  • the at least one genetic marker is selected from the group consisting of UBIAD1, LARS2, GJB2, HGF, MYO6, PCDH15, TMC1, MARVELD2, CDH23, OTOF, LRTOMT, LOXHD1, EDN3, MYO15A, SLC26A4, CLDN14, MARVELD2, WFS1, POU4F3, PTPRQ, SCARF2, COL4A4, USH2A, MYO7A and combinations thereof.
  • the details of the deafness panel are given below in Table 2.
  • the at least one genetic marker is selected from the group consisting of XPC, COL7A1, ALDH3A2, SLC39A4, CTSC, ITGB4, TGM1, HPS1, TYR, LAMBS, EOGT, DOCK6, LAMC2, GORAB, KRT5, KRT83, COL18A1, ALDH18A1, FERMT1, EOGT, DCAF17, DSP, NF1 and combinations thereof.
  • the details of the dermatological panel are given below in Table 3.
  • the at least one genetic marker is selected from the group consisting of LIFR, TCOF1, LARP7, EVC, POC1A, HGSNAT, COL2A1, CRTAP, COL11A2, DYM, COL1A1, CREBBP, COL11A1, PYCR1, NIPBL, ROR2, EXT1, ACTB, ADAMTSL2, NEK1, DYNC2H1, IRF6, NSD1, UBE3B, DLL3, EP300, SGSH, EZH2, CHRNG, GALNS, MGAT2, TNFRSF11B, LMNA, ERCC8, CANT1, MMP2, FKBP10, CUL7, GNPAT, FGFR2, FGFR3, MASP1, FREM1, HSPG2, MEOX1, OBSL1, WNT1, COL1A2, COL1A1, ANTXR2, PEX13, ECEL1, K
  • the at least one genetic marker is selected from the group consisting of TBCE, GHR, GHRHR, BBS5, SHOX and combinations thereof.
  • the details of the endocrine panel are given below in Table 5.
  • the at least one genetic marker is selected from the group consisting of UGT1A1, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9, JAG1, BAAT, ATP7B, TJP2, EPCAM, ABCB4, ABCC2, LRBA, SLC10A2, ABCB11, VIPAS39, FAH, G6PC and combinations thereof.
  • the details of the gastrointestinal panel are given below in Table 6.
  • the at least one genetic marker is selected from the group consisting of BLM, FANCA, FANCM, BRCA2, ASXL1 and combinations thereof.
  • BLM basic metal-oxide-semiconductor
  • FANCA hematoma-associated ANCA
  • FANCM hematoma-associated ANCM
  • the at least one genetic marker is selected from the group consisting of L2HGDH, MCCC2, SLC37A4, ARSB, HSD3B7, DBT, PHKG2, BTD, MUT, ASL, DPAGT1, ASAH1, AMT, BCKDHB, BCKDHA, CBS, PAH, CLN8, GBA, ACADM, SLC3A1, MMACHC, PTS, GNS, GCDH, SLC22A5, GAA, MMADHC, PYGL, ASS1, CPS1, H6PD, PTS, PGM1, IVD, ARG1, ASAH1, GLB1, OXCT1, OPLAH, FAH, G6PC, PEX1 and combinations thereof.
  • the details of the inborn errors of metabolism panel are given below in Table 8.
  • the at least one genetic marker is selected from the group consisting of L1CAM, ABCD1, DYSF, GBA2, TRAPPC9, CYP2U1, PANK2, ARL13B, KIF7, ERLIN2, PSAP, VAPB, FKTN, PLP1, GDAP1, ASPM, LAMA2, MECP2, CDK5RAP2, WDR81, ABAT, NDE1, WDR45B, HSD17B4, HEXA, SPG11, PDGFRB, HUWE1, SLC25A19, ARHGEF6, ADRA2B, RELN, CENPJ, ARL14EP, PHGDH, ARID1B, WNK1, SEPN1, RNASEH2C, RNASEH2B, CYP27A1, ATN1, AHI1, STXBP1, CDKL5, MED23, ISPD, CEP57, AGRN, FKRP, ADCK3, SCN2A, MFSD8, TYMP, FLVCR
  • the at least one genetic marker is selected from the group consisting of IL7R, JAK3, CD40LG, AK2, DCLRE1C, CD40, AICDA, MLPH, NHEJ1, RAB27A, RAG2, RAG1, BTK, ATM, LYST, CYBB, AIRE, DOCK8, SLC17A5, STAT3, WAS, CD247, DNMT3B, FLG, NCF2, ADA, RFXANK, PTPRC, COLEC11 and combinations thereof.
  • the details of the pelvic inflammatory disease panel are given below in Table 10.
  • the at least one genetic marker is selected from the group consisting of SFTPB, CFTR and combinations thereof.
  • SFTPB SFTPB
  • CFTR CFTR
  • the at least one genetic marker is selected from the group consisting of IQCB1, COL4A6, NPHP3, SLC4A4, DDX39A, SMARCAL1, PKHD1, LAMB2, NEK8, NPHP4, FRAS1, XDH, MKS1, FAN1, TCTN2, NPHS1, CC2D2A, TMEM231, UPK3A, CEP290, NPHP4, COL4A4, TMEM67, C5orf42, TMEM237 and combinations thereof.
  • the details of the renal panel are given below in Table 12.
  • the at least one genetic marker is selected from the group consisting of ALMS1, CRB1, CHST6, CRYBA1, PRSS56, GUCY2D, SNRNP200, PDE6C, CNGA3, C8orf37, ABCA4, BBS10, CERKL, GPR125, NHS, LTBP2, GCNT2, RLBP1, MIP, RP1L1, CHM, EYS, TULP1, IGFBP7, CYP1B1, LRAT, MERTK, CNNM4, RP1, RP2, LCA5, MFRP, CNGB1, CACNA1F, KCNV2, CRX, PROM1, TRPM1, PAX6, IMPG2, CDHR1, GPR179, CRYGC, CRYGD, NMNAT1, GALT, ARL6, LRP5, WDR19, SLC4A11, GDF3, SLC16A12, RGS9, RDH12, ADAMS, AIPL1, FAM161A, RPG
  • SNP genotyping arrays were used (Affymetrix Axiom GT1 chip with ⁇ 580,000 SNPs) coming from 21 patients as a second method of testing the analytical sensitivity.
  • the variants detected by SNP arrays were compared to those detected by the next generation sequencing (NGS) technology for each sample. From a total of 3,319 SNPs lying within the target regions of the panels, the resulting SNP sensitivity was about 95%. Interestingly, 30 extra SNPs were identified that were called by the assay but were not called with high confidence on the chip.
  • NGS next generation sequencing
  • a predetermined quality score of 100 was used (this takes into account strand-bias, homopolymer errors, etc.).
  • Analytical specificity was based on the Sanger validation of 1,078 variants called by the assay. Sanger sequencing confirmed 93% (819/881) of SNVs and 78% (154/197) of indels that met or were higher than that quality score.
  • PID Primary immunodeficiency
  • DD developmental delay
  • ID intellectual disability
  • RP retinitis pigmentosa
  • CRD cone-rod dystrophy
  • FEVR familial exudative vitreoretinopathy
  • GFS Goldmann-Favre syndrome
  • CHED corneal hereditary endothelial dystrophy
  • the clinical sensitivity of the Mendeliome assay (43%) is comparable to the ⁇ 25% reported by several large clinical whole exome sequencing (WES) studies.
  • the Mendeliome assay is inherently limited to established disease genes, so it will miss cases caused by large structural variants and mutations in novel genes, although the design is flexible and allows for the addition of newly published disease genes as frequently as needed, e.g. every six months. 213 cases were randomly selected that were negative by the Mendeliome assay, and these were processed using molecular karyotyping. Thirty-five of these were found to have likely pathogenic de novo copy-number variations (CNVs). If these 35 cases are excluded, the clinical sensitivity of the present method would increase slightly to 44%.
  • the cost is estimated to be $150 per sample with a range of $75-$150 per sample depending on the panel selected.
  • de novo mutations were identifiable as likely disease-causing heterozygous mutations in relevant Mendelian genes, and their de novo status was confirmed by Sanger sequencing of a single amplicon in both parents.
  • Also relevant to cost reduction is that five couples who lost children with a likely recessive disease were used, but there was no access to DNA from the deceased children. By running the appropriate panel on both parents the method was able to identify the likely causal mutation at a much lower cost than the duo WES design that would have been required to reach the same conclusion.
  • WES is frequently requested after one or more genes deemed relevant to the patient's clinical presentation had been excluded by Sanger sequencing in hopes of identifying a novel genetic cause.
  • many WES studies have highlighted the frequent encounter of disease-causing mutations in known genes that would not have been considered good candidates owing to the marked discrepancy between their published phenotype and the clinical presentation of the patient especially for neurological and dysmorphic disorders, which are often very heterogeneous clinically. It has been shown that even in familial cases that are carefully enriched for novel gene discovery by excluding all relevant candidate genes by autozygome analysis, 11% of WES will reveal mutations in known genes missed by the enrichment step because the presentation was very atypical.
  • GDD WDR45B Nonsense HMZ Inherited Neuro ID and microcephaly Primary Epilepsy (WDR45L) (Najmabadi et al, microcephaly White matter 2011) changes, brain atrophy, hypoplastic corpus callosum WDR81 Nonsense HMZ Inherited Neuro Cerebellar Cerebellar Normal corpus ataxia, Mental hypoplasia callosum retardation, and Prenatal onset Dysequilibrium complicated by syndrome 2 neonatal death (*)
  • Atypical case is defined as a case that has unusual clinical features, unusual mode of inheritance, a novel phenotype or lack of typical features.
  • DD Dysmorphia-Dysplasia Panel
  • GDD Global Developmental Delay
  • FTT Failure to Thrive
  • the above method was initially limited to genes that were very likely to be disease-causing in a Mendelian context (based on the best available evidence) in order to eliminate the uncertainty surrounding the finding of variants in genes not known to be linked to human diseases.
  • the study mainly included genes whose pathogenicity was supported by the presence of two pathogenic alleles. However, exceptions were made for genes with a single reported mutation but which were further supported by compelling mouse data or positional mapping data. This is important because it must be acknowledged that clinical WGS/WES currently appears to saddle the divide between clinical care and research.
  • the Mendeliome assay is negative, it may be easier to prepare the patient for the possibility of identifying a novel genetic cause by WGS/WES that requires confirmation in a research setting.
  • the present method seeks to be as inclusive as possible to minimize the challenge of atypical cases. For example, a gene for myopia presenting with ectopia lentis would still be identified because virtually every gene known to present with a prominent eye phenotype was included in the vision panel. In fact, the present analysis showed that only 3% (62/2,357) of cases may have been missed because the gene was not included in the right panel, and even this limitation can be addressed through a spike-in design.
  • the Mendeliome present symptom/sign based gene panels, collectively known as “The Mendeliome”, were designed in a way that simulates the way these patients present in clinical practice to the respective specialty.
  • Mendelian disorders are defined as hereditary disorders caused by a single autosomal or X-linked gene.
  • the OMIM database which currently contains about 4,300 monogenic disorders associated with known Molecular defects, represents the most comprehensive source of such information on monogenic disorders. Therefore, it was used as the primary source for gene identification. However, it was manually curated to ensure that only genes with confirmed links to disease are included. It was also supplemented with additional data from PubMed, Genetic Testing Registry (GTR), and gene tests. As such, the above 13 gene panels, which cover the spectrum of pediatric and adult clinical genetic medicine, were constructed. Within each panel, genes were sorted based on the most prominent sign/symptom with which they are most likely to be associated upon presentation to clinical care.
  • This presentation may help the referring clinician, and without requiring sophisticated knowledge about these genes, decide on the appropriateness of genetic testing using these gene panels. Since many genetic disorders are as likely to present to several medical specialties, the present method allows for redundancy between the different panels (average 15%) such that a gene may be present in more than one panel.
  • Primer design was based upon generating amplicons with an average length of 200 bp providing 90% minimum coverage of the coding DNA sequence (CDS) and on average 10 bp flanking regions of associated exons. Following this, in silico design coverage was assessed for compliance with design criteria and manual processes applied on a gene by gene basis to ensure adequate coverage and resolve factors such as 3′-SNPs that could impact primer efficiency. Primers for each panel were then synthesized and pooled into two multiplex reactions based upon polymerase chain reaction (PCR) compatibility minimizing likelihood of primer-primer interactions. Following this, synthesis primer pools were tested for coverage, recommended multiplexing and other quality control (QC) metrics to ensure specifications were met. Panels ranged from 96-758 gene with >90% coverage in 97-100% of genes in each panel.
  • CDS coding DNA sequence
  • the data of each run has been analyzed through a multistep pipeline.
  • the quality of the reads were verified and regions of the reads with low quality (less than 20) were trimmed out before alignment. The runs with low yield after this quality check were excluded.
  • the reads were aligned to the reference hg19 sequence. The observed depth after alignment ranges from 162X (for the neurology panel including 758 genes) to 840X (for the renal panel including 96 genes).
  • the aligned reads were processed for variant calling.
  • the variants were annotated using public knowledge databases as well as in-house variants databases.
  • the in-house databases include collections of disease-causing variants published by different Saudi teams and aggregation of the variants produced by the samples in this study.
  • the non-relevant variants were filtered out based on their functional characteristics and their abundance in the datasets. Variants that are less likely to play a functional role (intronic and synonymous) and variants that were present in population databases (e.g., in the 1000Genome database with MAF>1%) were filtered out. Furthermore, variants that were frequent in the in-house database were also filtered out; a variant with more than 20 occurrences was considered frequent. The cutoff of 20 occurrences was selected on test data to assure 100% sensitivity. An individual base quality of 100 (using Phred-like score) was also selected to exclude low confidence variants.
  • Table 16 shows the efficiency of the filtering strategy. Table 16 shows that the subsequent filtering steps lead to a short list of variants to be examined by domain experts. In this table, and as expected, the larger the panel, the larger the list. It is also important to note that more samples included in the in-house database leads to more filtration power and makes the list even shorter.
  • the recognized causal variant was identified as pathogenic or likely pathogenic as defined by the recent American College of Medical Genetics and Genomics (ACMG) guidelines, and the extensive variant data obtained by sequencing thousands of ethnically comparable patients (Saudis) was helpful in applying population frequency as a reliable criterion for pathogenicity in this study.
  • ACMG American College of Medical Genetics and Genomics
  • CytoScan HD arrays were used for the majority of the patients. This array platform contains 2.6 million markers for copy number variation (CNV) detection, of which 750,000 are genotype SNPs and 1.9 million are nonpolymorphic probes, for whole genome coverage. Briefly, 250 ng of genomic DNA was digested with the restriction enzyme NspI and then ligated to an adapter, followed by polymerase chain reaction (PCR) amplification using a single pair of primers that recognized the adapter sequence. The PCR products were run on a 2% Tris-borate-EDTA (TBE) gel to confirm that the majority of products were between 150 and 2,000 bp in length.
  • CNV copy number variation
  • the genic content in the CNV interval of all the patients who had a molecular karyotype performed was taken into consideration by seeking recent publications to compare breakpoints, phenotypes, and different sizes of CNVs that overlapped. To exclude aberrations representing common benign CNVs, all the identified CNVs were compared with those reported in the Database of Genomic Variants and those reported in the in-house database for individuals who have been classified as normal.
  • the remaining 178 were processed using WES.
  • One hundred nanograms of each DNA sample was treated to obtain the Ion Proton AmpliSeq library. Briefly, DNA was amplified in twelve separate wells with 10 amplification cycles. All twelve PCR pools were combined in one well and subjected to primer digestion performing incubation with FuPa reagent. Amplified exome targets were ligated with Ion P1 and Ion Xpress Barcode adapters. Following this, purification libraries were quantified using qPCR. The prepared exome library was further used for emulsion PCR and templated Ion Sphere particles were enriched using Ion OneTouch ES, both procedures following the manufacturer's instructions. The template-positive Ion PI Ion Sphere particles were processed for sequencing on the Ion Proton instrument. Approximately 15-17 Gb of sequence was generated per sequencing run.

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Wood Science & Technology (AREA)
  • Analytical Chemistry (AREA)
  • Zoology (AREA)
  • Genetics & Genomics (AREA)
  • Engineering & Computer Science (AREA)
  • Pathology (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The method of diagnosing patients with conditions caused by Mendelian mutations is a genetic panel-based diagnostic method for determining if a patient has a condition (or a proclivity for a condition) based on detection of one or more specific genetic markers. A sample is first obtained from a patient and the sample is assayed to determine the presence of at least one genetic marker. The assay is a sequencing-based multiplexing assay designed for the detection of specific Mendelian mutations. The patient is then diagnosed with a particular condition (or with a proclivity for that condition) if the at least one genetic marker is detected.

Description

    CROSS-REFERENCE TO RELATED APPLICATION
  • This application claims the benefit of U.S. Provisional Patent Application Ser. No. 62/156,872, filed on May 4, 2015, and which is hereby incorporated by reference in its entirety.
    • BACKGROUND OF THE INVENTION
  • 1. Field of the Invention
  • The present invention relates to genetic detection of conditions, and particularly to a method for diagnosing patients with conditions caused by Mendelian mutations, or diagnosing such patients as having a proclivity towards developing such conditions.
  • 2. Description of the Related Art
  • Genomics have ushered in a new era for clinical medicine. The ability to scan the entire genome (or its coding part) for disease causing mutations relatively free of clinical bias has uncovered the limited sensitivity and specificity of making diagnoses on clinical grounds only. This was first apparent with the advent of array-CGH that specifically targets large genomic mutations. Subsequently, whole genome sequencing (WGS) and whole exome sequencing (WES) confirmed the same pattern. This raises the interesting question of whether all patients with a suspected genetic diagnosis should have WGS/WES as the initial diagnostic test. Pending data on the validity of this approach, one has to consider some practical challenges. Cost remains a significant hurdle that prevents most patients, especially in less wealthy countries, from accessing WGS/WES. While the running cost will continue to decrease, the challenge of identifying a single causal variant from among tens of thousands will remain formidable for the foreseeable future. In addition, debate still rages over the issue of incidental findings with changing guidelines reflective of the strong and sound argument made by camps on either side of the debate, especially in pediatrics. Gene panels that specifically target a disease relevant to the patient's presentation appear to address some of these limitations but suffer from lack of uniformity in design and are typically too focused on a particular phenotype that they may miss atypical presentation. This is a particular issue when it comes to Mendelian mutations, which are single-gene mutations which may result in a wide variety of disorders. It would obviously be desirable to be able to develop an assay that addresses these limitations. Thus, a method of diagnosing patients with conditions caused by Mendelian mutations solving the aforementioned problems is desired.
    • SUMMARY OF THE INVENTION
  • The method of diagnosing patients with conditions caused by Mendelian mutations is a genetic panel-based diagnostic method for determining if a patient has a condition (or a proclivity for a condition) based on detection of one or more specific genetic markers. A sample is first obtained from a patient and the sample is assayed to determine the presence of at least one genetic marker. The assay is a sequencing-based multiplexing assay designed for the detection of specific Mendelian mutations (the set of which are referred to herein as the “Mendeliome”). The patient is then diagnosed with a particular condition (or with a proclivity for that condition) if the at least one genetic marker is detected.
  • For detection of cardiovascular disease (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of TTR, MYPN, TTN, COL4A3, KCNH2, SMAD4, NOTCH1, ANK2, PKP2, LDB3, MYH6, MYBPC3, SCN5A, MYL3, CACNA1C, DMD, BAG3, EHMT1, DSG2, ABCC9, KCNE2, RYR2, TTN, TTN-AS1, VCL, SOS1, ANKRD1, ACTN2, DSP, FBN1, CHD7 and combinations thereof.
  • For detection of deafness (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of UBIAD1, LARS2, GJB2, HGF, MYO6, PCDH15, TMC1, MARVELD2, CDH23, OTOF, LRTOMT, LOXHD1, EDN3, MYO15A, SLC26A4, CLDN14, MARVELD2, WFS1, POU4F3, PTPRQ, SCARF2, COL4A4, USH2A, MYO7A and combinations thereof.
  • For detection of dermatological conditions (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of XPC, COL7A1, ALDH3A2, SLC39A4, CTSC, ITGB4, TGM1, HPS1, TYR, LAMB3, EOGT, DOCK6, LAMC2, GORAB, KRT5, KRT83, COL18A1, ALDH18A1, FERMT1, EOGT, DCAF17, DSP, NF1 and combinations thereof.
  • For detection of dysmorphia-dysplasia (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of LIFR, TCOF1, LARP7, EVC, POC1A, HGSNAT, COL2A1, CRTAP, COL11A2, DYM, COL1A1, CREBBP, COL11A1, PYCR1, NIPBL, ROR2, EXT1, ACTB, ADAMTSL2, NEK1, DYNC2H1, IRF6, NSD1, UBE3B, DLL3, EP300, SGSH, EZH2, CHRNG, GALNS, MGAT2, TNFRSF11B, LMNA, ERCC8, CANT1, MMP2, FKBP10, CUL7, GNPAT, FGFR2, FGFR3, MASP1, FREM1, HSPG2, MEOX1, OBSL1, WNT1, COL1A2, COL1A1, ANTXR2, PEX13, ECEL1, KMT2A, KMT2D, PCNT, EBP, UBR1, WISP3, DLX5, IFT122, HRAS, SERPINF1, RIPK4, LEPRE1, BRAF, NFIX, FBN1, NF1, TMEM67, COLEC11, SCARF2 and combinations thereof.
  • For detection of endocrine conditions (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of TBCE, GHR, GHRHR, BBS5, SHOX and combinations thereof.
  • For detection of gastrointestinal conditions (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of UGT1A1, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9, JAG1, BAAT, ATP7B, TJP2, EPCAM, ABCB4, ABCC2, LRBA, SLC10A2, ABCB11, VIPAS39, FAH, G6PC and combinations thereof.
  • For detection of hematological conditions (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of BLM, FANCA, FANCM, BRCA2, ASXL1 and combinations thereof.
  • For detection of inborn errors of metabolism (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of L2HGDH, MCCC2, SLC37A4, ARSB, HSD3B7, DBT, PHKG2, BTD, MUT, ASL, DPAGT1, ASAH1, AMT, BCKDHB, BCKDHA, CBS, PAH, CLN8, GBA, ACADM, SLC3A1, MMACHC, PTS, GNS, GCDH, SLC22A5, GAA, MMADHC, PYGL, ASS1, CPS1, H6PD, PTS, PGM1, IVD, ARG1, ASAH1, GLB1, OXCT1, OPLAH, FAH, G6PC, PEX1 and combinations thereof.
  • For detection of neurological disorders (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of L1CAM, ABCD1, DYSF, GBA2, TRAPPC9, CYP2U1, PANK2, ARL13B, KIF7, ERLIN2, PSAP, VAPB, FKTN, PLP1, GDAP1, ASPM, LAMA2, MECP2, CDK5RAP2, WDR81, ABAT, NDE1, WDR45B, H5D17B4, HEXA, SPG11, PDGFRB, HUWE1, SLC25A19, ARHGEF6, ADRA2B, RELN, CENPJ, ARL14EP, PHGDH, ARID1B, WNK1, SEPN1, RNASEH2C, RNASEH2B, CYP27A1, ATN1, AHI1, STXBP1, CDKL5, MED23, ISPD, CEP57, AGRN, FKRP, ADCK3, SCN2A, MFSD8, TYMP, FLVCR2, SPG20, CACNA1G, PLA2G6, CLN6, WDR62, PEX26, KIF1A, PNPO, LARGE, YARS, KIAA0196, CCDC88C, OPTN, OCLN, ATRX, ATL1, GNE, PEX12, SPTBN2, PEX16, COL6A1, COL6A3, COL6A2, HEPACAM, LRPPRC, RYR1, NTRK1, CAPN3, SOD1, COG6, ATP2B3, DPYD, TUBA1A, TCTN1, CPA6, ABHD12, NPC2, MPDZ, SYNGAP1, PEX5, PEX6, POMT1, POMT2, MCPH1, CASC5, SGCB, SGCA, POMGNT2, TRMT1, ARFGEF2, SYNE2, ADK, ZNF526, FOXG1, ALS2, C5orf42, TMEM237, C12orf57, TMEM67, PEX1 and combinations thereof.
  • For detection of pelvic inflammatory disease (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of IL7R, JAK3, CD40LG, AK2, DCLRE1C, CD40, AICDA, MLPH, NHEJ1, RAB27A, RAG2, RAG1, BTK, ATM, LYST, CYBB, AIRE, DOCK8, SLC17A5, STATS, WAS, CD247, DNMT3B, FLG, NCF2, ADA, RFXANK, PTPRC, COLEC11 and combinations thereof.
  • For detection of pulmonary conditions (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of SFTPB, CFTR and combinations thereof.
  • For detection of renal conditions (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of IQCB1, COL4A6, NPHP3, SLC4A4, DDX39A, SMARCAL1, PKHD1, LAMB2, NEK8, NPHP4, FRAS1, XDH, MKS1, FAN1, TCTN2, NPHS1, CC2D2A, TMEM231, UPK3A, CEP290, NPHP4, COL4A4, TMEM67, C5orf42, TMEM237 and combinations thereof.
  • For detection of vision disorders (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of ALMS1, CRB1, CHST6, CRYBA1, PRSS56, GUCY2D, SNRNP200, PDE6C, CNGA3, C8orf37, ABCA4, BBS10, CERKL, GPR125, NHS, LTBP2, GCNT2, RLBP1, MIP, RP1L1, CHM, EYS, TULP1, IGFBP7, CYP1B1, LRAT, MERTK, CNNM4, RP1, RP2, LCA5, MFRP, CNGB1, CACNA1F, KCNV2, CRX, PROM1, TRPM1, PAX6, IMPG2, CDHR1, GPR179, CRYGC, CRYGD, NMNAT1, GALT, ARL6, LRP5, WDR19, SLC4A11, GDF3, SLC16A12, RGS9, RDH12, ADAMS, AIPL1, FAM161A, RPGRIP1, RAB3GAP2, RAB3GAP1, EFEMP1, BEST1, RPE65, EPHA2, FZD4, PRPH2, CRYAA, KCNJ13, NR2E3, BBS9, BBS1, BBS2, BBS5, BBS4, BBS7, SPATA7, CHD7, USH2A, MYO7A, C12orf57, CEP290, NPHP4 and combinations thereof.
  • These and other features of the present invention will become readily apparent upon further review of the following specification.
    • DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
  • The method of diagnosing patients with conditions caused by Mendelian mutations is a genetic panel-based diagnostic method for determining if a patient has a condition (or a proclivity for a condition) based on detection of one or more specific genetic markers. A sample is first obtained from a patient and the sample is assayed to determine the presence of at least one genetic marker. The assay is a sequencing-based multiplexing assay designed for the detection of specific Mendelian mutations (the set of which are referred to herein as the “Mendeliome”). The patient is then diagnosed with a particular condition (or with a proclivity for that condition) if the at least one genetic marker is detected.
  • For detection of cardiovascular disease (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of TTR, MYPN, TTN, COL4A3, KCNH2, SMAD4, NOTCH1, ANK2, PKP2, LDB3, MYH6, MYBPC3, SCN5A, MYL3, CACNA1C, DMD, BAG3, EHMT1, DSG2, ABCC9, KCNE2, RYR2, TTN, TTN-AS1, VCL, SOS1, ANKRD1, ACTN2, DSP, FBN1, CHD7 and combinations thereof. The details of the cardiovascular panel are given below in Table 1.
  • TABLE 1
    Cardiovascular Panel
    Number
    Gene Chr Start End Transcript of Exons MIM
    TTR chr18 29171729 29178986 NM_000371 4 176300
    MYPN chr10 69869189 69971773 NM_001256268 24 608517
    TTN chr2 179390716 179672150 NM_001267550 363 188840
    COL4A3 chr2 228029280 228179508 NM_000091 52 120070
    KCNH2 chr7 150642043 150675402 NM_000238 15 152427
    SMAD4 chr18 48556582 48611411 NM_005359 12 600993
    NOTCH1 chr9 139388895 139440238 NM_017617 34 190198
    ANK2 chr4 113970784 114304896 NM_001148 46 106410
    PKP2 chr12 32943679 33049780 NM_004572 14 602861
    LDB3 chr10 88428205 88495824 NM_001171610 14 605906
    MYH6 chr14 23851198 23877486 NM_002471 39 160710
    MYBPC3 chr11 47352956 47374253 NM_000256 34 600958
    SCN5A chr3 38589552 38691163 NM_198056 28 600163
    MYL3 chr3 46899356 46904973 NM_000258 7 160790
    CACNA1C chr12 2162415 2807115 NM_199460 50 114205
    DMD chrX 31137344 33038317 NM_004007 78 300377
    BAG3 chr10 121410881 121437329 NM_004281 4 603883
    EHMT1 chr9 140513443 140730578 NM_024757 27 607001
    DSG2 chr18 29078026 29128814 NM_001943 15 125671
    ABCC9 chr12 21958107 22089628 NM_005691 38 601439
    KCNE2 chr21 35736322 35743440 NM_172201 2 603796
    RYR2 chr1 237205701 237997288 NM_001035 105 180902
    TTN chr2 179390716 179672150 NM_001267550 363 188840
    TTN-AS1 chr2 179385910 179644690 NR_038271 7 NA
    VCL chr10 75757871 75879914 NM_014000 22 193065
    SOS1 chr2 39208689 39347604 NM_005633 23 182530
    ANKRD1 chr10 92671856 92681032 NM_014391 9 609599
    ACTN2 chr1 236849753 236927927 NM_001278344 23 102573
  • For detection of deafness (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of UBIAD1, LARS2, GJB2, HGF, MYO6, PCDH15, TMC1, MARVELD2, CDH23, OTOF, LRTOMT, LOXHD1, EDN3, MYO15A, SLC26A4, CLDN14, MARVELD2, WFS1, POU4F3, PTPRQ, SCARF2, COL4A4, USH2A, MYO7A and combinations thereof. The details of the deafness panel are given below in Table 2.
  • TABLE 2
    Deafness Panel
    Number
    of
    Gene Chr Start End Transcript Exons MIM
    UBIAD1 chr1 11333254 11348491 NM_013319 2 611632
    LARS2 chr3 45430074 45590328 NM_015340 22 604544
    GJB2 chr13 20761603 20767114 NM_004004 2 121011
    HGF chr7 81331443 81399452 NM_000601 18 142409
    MYO6 chr6 76458908 76629254 NM_004999 35 600970
    PCDH15 chr10 55568451 56561051 NM_001142769 36 605514
    TMC1 chr9 75136716 75451267 NM_138691 24 606706
    MARVELD2 chr5 68710938 68737890 NM_001038603 7 610572
    CDH23 chr10 73156690 73575704 NM_022124 68 605516
    OTOF chr2 26680070 26781566 NM_194248 47 603681
    LRTOMT chr11 71791376 71821828 NM_001145309 9 612414
    LOXHD1 chr18 44057216 44236996 NM_144612 40 613072
    EDN3 chr20 57875498 57901047 NM_000114 6 131242
    MYO15A chr17 18012019 18083116 NM_016239 65 602666
    SLC26A4 chr7 107301079 107358252 NM_000441 21 605646
    CLDN14 chr21 37832919 37948867 NM_001146077 3 605608
    MARVELD2 chr5 68710938 68737890 NM_001038603 7 610572
    WFS1 chr4 6271576 6304992 NM_001145853 8 606201
    POU4F3 chr5 145718586 145720083 NM_002700 2 602460
    PTPRQ chr12 80838125 81073968 NM_001145026 42 603317
    SCARF2 chr22 20778873 20792146 NM_182895 11 613619
    COL4A4 chr2 227867426 228029275 NM_000092 48 120131
    USH2A chr1 215796235 216596738 NM_206933 72 608400
    MYO7A chr11 76839309 76926286 NM_000260 49 276903
  • For detection of dermatological conditions (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of XPC, COL7A1, ALDH3A2, SLC39A4, CTSC, ITGB4, TGM1, HPS1, TYR, LAMBS, EOGT, DOCK6, LAMC2, GORAB, KRT5, KRT83, COL18A1, ALDH18A1, FERMT1, EOGT, DCAF17, DSP, NF1 and combinations thereof. The details of the dermatological panel are given below in Table 3.
  • TABLE 3
    Dermatological Panel
    Number
    of
    Gene Chr Start End Transcript Exons MIM
    XPC chr3 14186647 14220172 NM_001145769 16 613208
    COL7A1 chr3 48601505 48632593 NM_000094 118 120120
    ALDH3A2 chr17 19552063 19580904 NM_001031806 11 609523
    SLC39A4 chr8 145637797 145642273 NM_130849 12 607059
    CTSC chr11 88026759 88070941 NM_001814 7 602365
    ITGB4 chr17 73717515 73753899 NM_000213 40 147557
    TGM1 chr14 24718319 24732416 NM_000359 15 190195
    HPS1 chr10 100188902 100206704 NM_182639 10 604982
    TYR chr11 88911039 89028927 NM_000372 5 606933
    LAMB3 chr1 209788217 209825674 NM_001127641 23 150310
    EOGT chr3 69024365 69063112 NM_001278689 18 614789
    DOCK6 chr19 11309968 11373168 NM_020812 48 614194
    LAMC2 chr1 183155173 183210406 NM_018891 22 150292
    GORAB chr1 170501262 170522974 NR_027397 5 607983
    KRT5 chr12 52908358 52914243 NM_000424 9 148040
    KRT83 chr12 52708084 52715182 NM_002282 9 602765
    COL18A1 chr21 46875423 46933634 NM_030582 42 120328
    ALDH18A1 chr10 97365685 97416567 NM_001017423 18 138250
    FERMT1 chr20 6055491 6104191 NM_017671 15 607900
    EOGT chr3 69024365 69063112 NM_001278689 18 614789
    DCAF17 chr2 172290760 172341562 NM_025000 14 612515
    DSP chr6 7541869 7586946 NM_004415 24 125647
  • For detection of dysmorphia-dysplasia (DD) (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of LIFR, TCOF1, LARP7, EVC, POC1A, HGSNAT, COL2A1, CRTAP, COL11A2, DYM, COL1A1, CREBBP, COL11A1, PYCR1, NIPBL, ROR2, EXT1, ACTB, ADAMTSL2, NEK1, DYNC2H1, IRF6, NSD1, UBE3B, DLL3, EP300, SGSH, EZH2, CHRNG, GALNS, MGAT2, TNFRSF11B, LMNA, ERCC8, CANT1, MMP2, FKBP10, CUL7, GNPAT, FGFR2, FGFR3, MASP1, FREM1, HSPG2, MEOX1, OBSL1, WNT1, COL1A2, COL1A1, ANTXR2, PEX13, ECEL1, KMT2A, KMT2D, PCNT, EBP, UBR1, WISP3, DLX5, IFT122, HRAS, SERPINF1, RIPK4, LEPRE1, BRAF, NFIX, FBN1, NF1, TMEM67, COLEC11, SCARF2 and combinations thereof. The details of the dysmorphia-dysplasia panel are given below in Table 4.
  • TABLE 4
    Dysmorphia-Dysplasia (DD) Panel
    Number
    of
    Gene Chr Start End Transcript Exons MIM
    LIFR chr5 38475064 38595507 NM_002310 20 151443
    TCOF1 chr5 149737201 149779871 NM_001135243 27 606847
    LARP7 chr4 113558119 113578748 NM_001267039 15 612026
    EVC chr4 5712923 5816031 NM_153717 21 604831
    POC1A chr3 52109248 52188706 NM_015426 11 614783
    HGSNAT chr8 42995591 43057970 NM_152419 18 610453
    COL2A1 chr12 48366747 48398285 NM_001844 54 120140
    CRTAP chr3 33155449 33189265 NM_006371 7 605497
    COL11A2 chr6 4610635 4637414 NM_080680 65 120290
    DYM chr18 46570171 46987079 NM_017653 17 607461
    COL1A1 chr17 48261456 48279000 NM_000088 51 120150
    CREBBP chr16 3775055 3930121 NM_004380 31 600140
    COL11A1 chr1 103342022 103574052 NM_080629 67 120280
    PYCR1 chr17 79890266 79894968 NM_153824 8 179035
    NIPBL chr5 36876860 37065921 NM_133433 47 608667
    ROR2 chr9 94484877 94712444 NM_004560 9 602337
    EXT1 chr8 118811601 119124058 NM_000127 11 608177
    ACTB chr7 5566778 5570232 NM_001101 6 102630
    ADAMTSL2 chr9 136399974 136440641 NM_014694 19 612277
    NEK1 chr4 170314420 170533778 NM_001199397 36 604588
    DYNC2H1 chr11 102980159 103350591 NM_001080463 90 603297
    IRF6 chr1 209958967 209979520 NM_006147 9 607199
    NSD1 chr5 176560832 176727214 NM_022455 23 606681
    UBE3B chr12 109915427 109974510 NM_183415 28 608047
    DLL3 chr19 39989556 39999121 NM_203486 9 602768
    EP300 chr22 41488613 41576081 NM_001429 31 602700
    SGSH chr17 78183078 78194199 NM_000199 8 605270
    EZH2 chr7 148504463 148581441 NM_001203247 20 601573
    CHRNG chr2 233404436 233411038 NM_005199 12 100730
    GALNS chr16 88880141 88923374 NM_000512 14 612222
    MGAT2 chr14 50087488 50090199 NM_002408 1 602616
    TNFRSF11B chr8 119935795 119964383 NM_002546 5 602643
    LMNA chr1 156095950 156109880 NM_001257374 13 150330
    ERCC8 chr5 60169658 60240905 NM_000082 12 609412
    CANT1 chr17 76987797 77005899 NM_001159773 5 613165
    MMP2 chr16 55513080 55540586 NM_004530 13 120360
    FKBP10 chr17 39968961 39979469 NM_021939 10 607063
    CUL7 chr6 43005354 43021683 NM_001168370 26 609577
    GNPAT chr1 231376918 231413719 NM_014236 16 602744
    FGFR2 chr10 123241366 123353481 NM_001144913 17 176943
    FGFR3 chr4 1795038 1810599 NM_001163213 18 134934
    MASP1 chr3 186933872 187009810 NM_001879 16 600521
    FREM1 chr9 14734663 14910993 NM_144966 38 608944
    HSPG2 chr1 22148736 22263750 NM_005529 97 142461
    MEOX1 chr17 41717757 41738931 NM_004527 3 600147
    OBSL1 chr2 220415449 220436268 NM_015311 21 610991
    WNT1 chr12 49372235 49376396 NM_005430 4 164820
    COL1A2 chr7 94023872 94060544 NM_000089 52 120160
    COL1A1 chr17 48261456 48279000 NM_000088 51 120150
    ANTXR2 chr4 80898661 80994477 NM_001145794 16 608041
    PEX13 chr2 61244811 61279125 NM_002618 4 601789
    ECEL1 chr2 233344536 233352532 NM_004826 18 605896
    KMT2A 11 118307205 118397539 NM_001197104 36 159555
    KMT2D chr12 49412758 49453557 NM_003482 54 602113
    PCNT chr21 47744035 47865682 NM_006031 47 605925
    EBP chrX 48380163 48387104 NM_006579 5 300205
    UBR1 chr15 43235097 43398286 NM_174916 47 605981
    WISP3 chr6 112375277 112390887 NM_003880 6 603400
    DLX5 chr7 96649701 96654143 NM_005221 3 600028
    IFT122 chr3 129158967 129239191 NM_052985 31 606045
    HRAS chr11 532241 535550 NM_005343 6 190020
    SERPINF1 chr17 1665258 1680859 NM_002615 8 172860
    RIPK4 chr21 43159528 43187249 NM_020639 8 605706
    LEPRE1 chr1 43212005 43232755 NM_022356 15 610339
    BRAF chr7 140433812 140624564 NM_004333 18 164757
    NFIX chr19 13135394 13209610 NM_001271043 11 164005
    FBN1 chr15 48700502 48937985 NM_000138 66 134797
    NF1 chr17 29421944 29704695 NM_001042492 58 613113
    TMEM67 chr8 94767071 94831460 NR_024522 29 609884
    COLEC11 chr2 3642421 3692234 NM_199235 8 612502
  • For detection of endocrine conditions (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of TBCE, GHR, GHRHR, BBS5, SHOX and combinations thereof. The details of the endocrine panel are given below in Table 5.
  • TABLE 5
    Endocrine Panel
    Number
    of
    Gene Chr Start End Transcript Exons MIM
    TBCE chr1 235530727 235612280 NM_003193 17 604934
    GHR chr5 42424553 42721980 NM_001242399 10 600946
    GHRHR chr7 31003635 31019146 NM_000823 13 139191
    BBS5 chr2 170336005 170363165 NM_152384 12 603650
    SHOX chrX 535078 570146 NM_006883 6 400020
  • For detection of gastrointestinal (GI) conditions (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of UGT1A1, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9, JAG1, BAAT, ATP7B, TJP2, EPCAM, ABCB4, ABCC2, LRBA, SLC10A2, ABCB11, VIPAS39, FAH, G6PC and combinations thereof. The details of the gastrointestinal panel are given below in Table 6.
  • TABLE 6
    Gastrointestinal (GI) Panel
    Number
    of
    Gene Chr Start End Transcript Exons MIM
    UGT1A1 chr2 234668894 234681945 NM_000463 5 191740
    UGT1A10 chr2 234545100 234681951 NM_019075 5 606435
    UGT1A3 chr2 234637754 234681945 NM_019093 5 606428
    UGT1A4 chr2 234627437 234681945 NM_007120 5 606429
    UGT1A5 chr2 234621638 234681945 NM_019078 5 606430
    UGT1A6 chr2 234600253 234681946 NM_001072 5 606431
    UGT1A7 chr2 234601511 234681951 NM_001072 5 606432
    UGT1A8 chr2 234526291 234681956 NM_019076 5 606433
    UGT1A9 chr2 234580499 234681946 NM_021027 5 606434
    JAG1 chr20 10618331 10654694 NM_000214 26 601920
    BAAT chr9 104122698 104147287 NM_001701 4 602938
    ATP7B chr13 52506805 52585630 NM_000053 21 606882
    TJP2 chr9 71820077 71870124 NM_001170416 23 607709
    EPCAM chr2 47596286 47614167 NM_002354 9 185535
    ABCB4 chr7 87031360 87105019 NM_018849 28 171060
    ABCC2 chr10 101542462 101611662 NM_000392 32 601107
    LRBA chr4 151185810 151936649 NM_006726 58 606453
    SLC10A2 chr13 103696347 103719196 NM_000452 6 601295
    ABCB11 chr2 169779448 169887833 NM_003742 28 603201
    VIPAS39 chr14 77893018 77924295 NM_022067 21 613401
  • For detection of hematological conditions (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of BLM, FANCA, FANCM, BRCA2, ASXL1 and combinations thereof. The details of the hematology panel are given below in Table 7.
  • TABLE 7
    Hematology Panel
    Num-
    ber of
    Ex-
    Gene Chr Start End Transcript ons MIM
    BLM chr15 91260578 91358686 NM_000057 22 604610
    FANCA chr16 89803958 89883065 NM_000135 43 607139
    FANCM chr14 45605135 45670093 NM_020937 23 609644
    BRCA2 chr13 32889616 32973809 NM_000059 27 600185
    ASXL1 chr20 30946146 31027122 NM_015338 12 612990
  • For detection of inborn errors of metabolism (IBM) (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of L2HGDH, MCCC2, SLC37A4, ARSB, HSD3B7, DBT, PHKG2, BTD, MUT, ASL, DPAGT1, ASAH1, AMT, BCKDHB, BCKDHA, CBS, PAH, CLN8, GBA, ACADM, SLC3A1, MMACHC, PTS, GNS, GCDH, SLC22A5, GAA, MMADHC, PYGL, ASS1, CPS1, H6PD, PTS, PGM1, IVD, ARG1, ASAH1, GLB1, OXCT1, OPLAH, FAH, G6PC, PEX1 and combinations thereof. The details of the inborn errors of metabolism panel are given below in Table 8.
  • TABLE 8
    Inborn Errors of Metabolism (IEM) Panel
    Number
    of
    Gene Chr Start End Transcript Exons MIM
    L2HGDH chr14 50709151 50778947 NM_024884 10 609584
    MCCC2 chr5 70883114 70954530 NM_022132 17 609014
    SLC37A4 chr11 118895060 118901616 NM_001164279 11 602671
    ARSB chr5 78111333 78281766 NM_198709 8 611542
    HSD3B7 chr16 30996518 31000473 NM_025193 7 607764
    DBT chr1 100652477 100715409 NM_001918 11 248610
    PHKG2 chr16 30759619 30772497 NM_001172432 11 172471
    BTD chr3 15643254 15687325 NM_000060 4 609019
    MUT chr6 49398072 49431041 NM_000255 13 609058
    ASL chr7 65540775 65558329 NM_000048 17 608310
    DPAGT1 chr11 118967212 118972785 NM_001382 9 191350
    ASAH1 chr8 17913924 17942507 NM_004315 14 613468
    AMT chr3 49454210 49460111 NM_001164712 10 238310
    BCKDHB chr6 80816343 81055987 NM_000056 11 248611
    BCKDHA chr19 41937222 41945843 NM_018035 6 608348
    CBS chr21 44473300 44496472 NM_001178009 18 613381
    PAH chr12 103232103 103311381 NM_000277 13 612349
    CLN8 chr8 1711869 1734736 NM_018941 3 607837
    GBA chr1 155204238 155214653 NM_001005742 12 606463
    ACADM chr1 76190042 76229355 NM_001127328 12 607008
    SLC3A1 chr2 44502596 44547962 NM_000341 10 104614
    MMACHC chr1 45965855 45976739 NM_015506 4 609831
    PTS chr11 112097087 112104695 NM_000317 6 612719
    GNS chr12 65107221 65153226 NM_002076 14 607664
    GCDH chr19 13001942 13010813 NM_013976 12 608801
    SLC22A5 chr5 131705400 131731306 NM_003060 10 603377
    GAA chr17 78075354 78093679 NM_001079804 20 606800
    MMADHC chr2 150426146 150444330 NM_015702 8 611935
    PYGL chr14 51371934 51411248 NM_002863 20 613741
    ASS1 chr9 133320093 133376661 NM_000050 16 603470
    CPS1 chr2 211342405 211543831 NM_001122633 39 608307
    H6PD chr1 9294862 9331394 NM_004285 5 138090
    PTS chr11 112097087 112104695 NM_000317 6 612719
    PGM1 chr1 64088886 64125916 NM_001172818 11 171900
    IVD chr15 40697685 40713512 NM_002225 12 607036
    ARG1 chr6 131894343 131905472 NM_001244438 8 608313
    ASAH1 chr8 17913924 17942507 NM_004315 14 613468
    GLB1 chr3 33038099 33138314 NM_001079811 16 611458
    OXCT1 chr5 41730166 41870791 NM_000436 17 601424
    OPLAH chr8 145106166 145115584 NM_017570 28 614243
    FAH chr15 80445232 80478924 NM_000137 14 613871
    G6PC chr17 41052813 41066450 NM_000151 5 613742
    PEX1 chr7 92116336 92157845 NM_000466 24 602136
  • For detection of neurological disorders (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of L1CAM, ABCD1, DYSF, GBA2, TRAPPC9, CYP2U1, PANK2, ARL13B, KIF7, ERLIN2, PSAP, VAPB, FKTN, PLP1, GDAP1, ASPM, LAMA2, MECP2, CDK5RAP2, WDR81, ABAT, NDE1, WDR45B, HSD17B4, HEXA, SPG11, PDGFRB, HUWE1, SLC25A19, ARHGEF6, ADRA2B, RELN, CENPJ, ARL14EP, PHGDH, ARID1B, WNK1, SEPN1, RNASEH2C, RNASEH2B, CYP27A1, ATN1, AHI1, STXBP1, CDKL5, MED23, ISPD, CEP57, AGRN, FKRP, ADCK3, SCN2A, MFSD8, TYMP, FLVCR2, SPG20, CACNA1G, PLA2G6, CLN6, WDR62, PEX26, KIF1A, PNPO, LARGE, YARS, KIAA0196, CCDC88C, OPTN, OCLN, ATRX, ATL1, GNE, PEX12, SPTBN2, PEX16, COL6A1, COL6A3, COL6A2, HEPACAM, LRPPRC, RYR1, NTRK1, CAPN3, SOD1, COG6, ATP2B3, DPYD, TUBA1A, TCTN1, CPA6, ABHD12, NPC2, MPDZ, SYNGAP1, PEX5, PEX6, POMT1, POMT2, MCPH1, CASC5, SGCB, SGCA, POMGNT2, TRMT1, ARFGEF2, SYNE2, ADK, ZNF526, FOXG1, ALS2, C5orf42, TMEM237, C12orf57, TMEM67, PEX1 and combinations thereof. The details of the neurological panel are given below in Table 9.
  • TABLE 9
    Neurological Panel
    Number
    of
    Gene Chr Start End Transcript Exons MIM
    L1CAM chrX 153126968 153151628 NM_001278116 29 308840
    ABCD1 chrX 152990322 153010216 NM_000033 10 300371
    DYSF chr2 71693831 71913893 NM_001130983 56 603009
    GBA2 chr9 35736862 35749225 NM_020944 17 609471
    TRAPPC9 chr8 140742585 141468678 NM_031466 23 611966
    CYP2U1 chr4 108852716 108874613 NM_183075 5 610670
    PANK2 chr20 3869741 3904502 NM_153638 7 606157
    ARL13B chr3 93698982 93774522 NM_182896 11 608922
    KIF7 chr15 90171200 90198682 NM_198525 19 611254
    ERLIN2 chr8 37594096 37615319 NM_007175 12 611605
    PSAP chr10 73576054 73611082 NM_001042465 15 176801
    VAPB chr20 56964174 57026156 NM_004738 6 605704
    FKTN chr9 108320410 108403399 NM_001198963 12 607440
    PLP1 chrX 103031753 103047547 NM_000533 7 300401
    GDAP1 chr8 75262617 75279335 NM_018972 6 606598
    ASPM chr1 197053256 197115824 NM_018136 28 605481
    LAMA2 chr6 129204285 129837710 NM_000426 65 156225
    MECP2 chrX 153295685 153363188 NM_001110792 3 300005
    CDK5RAP2 chr9 123151146 123342448 NR_073556 39 608201
    WDR81 chr17 1628124 1641893 NM_001163809 10 614218
    ABAT chr16 8768443 8878432 NM_020686 16 137150
    NDE1 chr16 15737124 15820210 NM_017668 9 609449
    WDR45B chr17 80572438 80606429 NM_019613 10 609226
    HSD17B4 chr5 118788201 118878030 NM_001199291 25 601860
    HEXA chr15 72635777 72668520 NM_000520 14 606869
    SPG11 chr15 44854893 44955876 NM_025137 40 610844
    PDGFRB chr5 149493401 149535422 NM_002609 23 173410
    HUWE1 chrX 53559056 53713697 NM_031407 84 300697
    SLC25A19 chr17 73269060 73285530 NM_001126122 7 606521
    ARHGEF6 chrX 135747711 135863503 NM_004840 22 300267
    ADRA2B chr2 96778622 96781888 NM_000682 1 104260
    RELN chr7 103112230 103629963 NM_005045 65 600514
    CENPJ chr13 25456411 25497027 NR_047594 18 609279
    ARL14EP chr11 30344598 30359774 NM_152316 4 612295
    PHGDH chr1 120254418 120286849 NM_006623 12 606879
    ARID1B chr6 157099063 157531913 NM_020732 20 614556
    WNK1 chr12 862088 1020618 NM_018979 28 605232
    SEPN1 chr1 26126666 26144713 NM_020451 13 606210
    RNASEH2C chr11 65485143 65488409 NM_032193 4 610330
    RNASEH2B chr13 51483813 51530901 NM_024570 11 610326
    CYP27A1 chr2 219646471 219680016 NM_000784 9 606530
    ATN1 chr12 7033625 7051484 NM_001007026 10 607462
    AHI1 chr6 135708921 135818903 NM_001134832 23 608894
    STXBP1 chr9 130374485 130454995 NM_001032221 19 602926
    CDKL5 chrX 18460343 18671749 NM_001037343 22 300203
    MED23 chr6 131907877 131949379 NM_001270522 30 605042
    ISPD chr7 16127151 16460947 NM_001101426 10 614631
    CEP57 chr11 95523624 95565857 NM_001243776 12 607951
    AGRN chr1 955502 991499 NM_198576 36 103320
    FKRP chr19 47249302 47261832 NM_001039885 4 606596
    ADCK3 chr1 227127937 227175246 NM_020247 15 606980
    SCN2A chr2 166095911 166248820 NM_001040142 27 182390
    MFSD8 chr4 128838959 128887139 NM_152778 13 611124
    TYMP chr22 50964180 50968514 NM_001257989 10 131222
    FLVCR2 chr14 76044939 76114512 NM_017791 10 610865
    SPG20 chr13 36875774 36944317 NM_001142294 9 607111
    CACNA1G chr17 48638428 48704832 NM_018896 38 604065
    PLA2G6 chr22 38507501 38577761 NM_003560 17 603604
    CLN6 chr15 68499329 68522080 NM_017882 7 606725
    WDR62 chr19 36545782 36596012 NM_173636 32 613583
    PEX26 chr22 18560759 18573797 NM_001127649 5 608666
    KIF1A chr2 241653180 241759725 NM_001244008 49 601255
    PNPO chr17 46018888 46026674 NM_018129 7 603287
    LARGE chr22 33669061 34316416 NM_133642 15 603590
    YARS chr1 33240839 33283633 NM_003680 13 603623
    KIAA0196 chr8 126036502 126104061 NM_014846 29 610657
    CCDC88C chr14 91737666 91884188 NM_001080414 30 611204
    OPTN chr10 13142081 13180276 NM_001008213 16 602432
    OCLN chr5 68788589 68853931 NM_001205254 9 602876
    ATRX chrX 76760355 77041719 NM_000489 35 300032
    ATL1 chr14 50999799 51099784 NM_001127713 14 606439
    GNE chr9 36214438 36277053 NM_001128227 12 603824
    PEX12 chr17 33901813 33905656 NM_000286 3 601758
    SPTBN2 chr11 66452719 66488870 NM_006946 37 604985
    PEX16 chr11 45931219 45939674 NM_057174 11 603360
    COL6A1 chr21 47401662 47424963 NM_001848 35 120220
    COL6A3 chr2 238232654 238322850 NM_004369 44 120250
    COL6A2 chr21 47518032 47552763 NM_001849 28 120240
    HEPACAM chr11 124789145 124806308 NM_152722 7 611642
    LRPPRC chr2 44113362 44223144 NM_133259 38 607544
    RYR1 chr19 38924339 39078204 NM_000540 106 180901
    NTRK1 chr1 156830670 156851642 NM_002529 17 191315
    CAPN3 chr15 42651697 42704515 NM_000070 24 114240
    SOD1 chr21 33031934 33041243 NM_000454 5 147450
    COG6 chr13 40229763 40326765 NR_026745 20 606977
    ATP2B3 chrX 152801579 152848387 NM_021949 21 300014
    DPYD chr1 97543299 98386615 NM_000110 23 612779
    TUBA1A chr12 49578577 49583107 NM_006009 4 602529
    TCTN1 chr12 111051911 111086935 NM_001173975 15 609863
    CPA6 chr8 68334404 68658620 NM_020361 11 609562
    ABHD12 chr20 25275378 25371618 NM_015600 13 613599
    NPC2 chr14 74946642 74960084 NM_006432 5 601015
    MPDZ chr9 13105702 13279563 NM_001261406 46 603785
    SYNGAP1 chr6 4868092 4901710 NM_006772 19 603384
    PEX5 chr12 7341758 7371169 NM_001131026 18 600414
    PEX6 chr6 42931610 42946981 NM_000287 17 601498
    POMT1 chr9 134378288 134399193 NM_001077365 20 607423
    POMT2 chr14 77741298 77787225 NM_013382 21 607439
    MCPH1 chr8 6264112 6501140 NM_024596 14 607117
    CASC5 chr15 40886446 40954881 NM_170589 27 609173
    SGCB chr4 152886860 52904485 NM_000232 6 600900
    SGCA chr17 48243365 48253293 NM_000023 10 600119
    POMGNT2 chr3 43120724 43147568 NM_032806 2 614828
    TRMT1 chr19 13215713 13227563 NM_001136035 17 611669
    ARFGEF2 chr20 47538274 47653230 NM_006420 39 605371
    SYNE2 chr14 64319682 64693167 NM_182914 116 608442
    ADK chr10 75910942 76469061 NM_006721 11 102750
    ZNF526 chr19 42724491 42732353 NM_133444 3 614387
    FOXG1 chr14 29236277 29239483 NM_005249 1 164874
    ALS2 chr2 202564985 202645895 NM_020919 34 606352
    C5orf42 chr5 37106329 37249530 NM_023073 52 614571
    TMEM237 chr2 202484906 202508252 NM_001044385 12 614423
    C12orf57 chr12 7053202 7055165 NM_138425 3 615140
  • For detection of pelvic inflammatory disease (PID) (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of IL7R, JAK3, CD40LG, AK2, DCLRE1C, CD40, AICDA, MLPH, NHEJ1, RAB27A, RAG2, RAG1, BTK, ATM, LYST, CYBB, AIRE, DOCK8, SLC17A5, STAT3, WAS, CD247, DNMT3B, FLG, NCF2, ADA, RFXANK, PTPRC, COLEC11 and combinations thereof. The details of the pelvic inflammatory disease panel are given below in Table 10.
  • TABLE 10
    Pelvic Inflammatory Disease (PID) Panel
    Number
    of
    Gene Chr Start End Transcript Exons MIM
    IL7R chr5 35856976 35879705 NM_002185 8 146661
    JAK3 chr19 17935592 17958841 NM_000215 24 600173
    CD40LG chrX 135730335 135742549 NM_000074 5 300386
    AK2 chr1 33473540 33502512 NR_037591 8 103020
    DCLRE1C chr10 14948870 14996094 NM_001033858 16 605988
    CD40 chr20 44746905 44758384 NM_001250 9 109535
    AICDA chr12 8754761 8765442 NM_020661 5 605257
    MLPH chr2 238395877 238463961 NM_024101 16 606526
    NHEJ1 chr2 219940045 220025587 NM_024782 8 611290
    RAB27A chr15 55495163 55582013 NM_183235 7 603868
    RAG2 chr11 36613492 36619829 NM_000536 2 179616
    RAG1 chr11 36589562 36601310 NM_000448 2 179615
    BTK chrX 100604434 100641212 NM_000061 19 300300
    ATM chr11 108093558 108239826 NM_000051 63 607585
    LYST chr1 235824330 236030227 NM_000081 53 606897
    CYBB chrX 37639269 37672714 NM_000397 13 300481
    AIRE chr21 45705720 45718102 NM_000383 14 607358
    DOCK8 chr9 214864 465259 NM_203447 48 611432
    SLC17A5 chr6 74303101 74363737 NM_012434 11 604322
    STAT3 chr17 40465342 40540405 NM_213662 24 102582
    WAS chrX 48542185 48549817 NM_000377 12 300392
    CD247 chr1 167399876 167487847 NM_198053 8 186780
    DNMT3B chr20 31350190 31397162 NM_006892 23 602900
    FLG chr1 152274650 152297679 NM_002016 3 135940
    NCF2 chr1 183524696 183560056 NM_001127651 16 608515
    ADA chr20 43248162 43280376 NM_000022 12 608958
    RFXANK chr19 19303007 19312678 NM_003721 10 603200
    PTPRC chr1 198608097 198726605 NM_002838 33 151460
  • For detection of pulmonary conditions (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of SFTPB, CFTR and combinations thereof. The details of the pulmonary panel are given below in Table 11.
  • TABLE 11
    Pulmonary Panel
    Gene Chr Start End Transcript Number of Exons MIM
    SFTPB chr2 85884439 85895864 NM_000542 12 178640
    CFTR chr7 117120016 117308718 NM_000492 27 602421
  • For detection of renal conditions (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of IQCB1, COL4A6, NPHP3, SLC4A4, DDX39A, SMARCAL1, PKHD1, LAMB2, NEK8, NPHP4, FRAS1, XDH, MKS1, FAN1, TCTN2, NPHS1, CC2D2A, TMEM231, UPK3A, CEP290, NPHP4, COL4A4, TMEM67, C5orf42, TMEM237 and combinations thereof. The details of the renal panel are given below in Table 12.
  • TABLE 12
    Renal Panel
    Number
    of
    Gene Chr Start End Transcript Exons MIM
    IQCB1 chr3 121488609 121553926 NM_001023570 15 609237
    COL4A6 chrX 107398836 107682704 NM_001847 45 303631
    NPHP3 chr3 132399452 132441303 NM_153240 27 608002
    SLC4A4 chr4 72053002 72437804 NM_001098484 26 603345
    DDX39A chr19 14519609 14529906 NR_038336 12 NA
    SMARCAL1 chr2 217277472 217347774 NM_001127207 18 606622
    PKHD1 chr6 51585646 51952423 NM_170724 61 606702
    LAMB2 chr3 49158546 49170599 NM_002292 32 150325
    NEK8 chr17 27055831 27069784 NM_178170 15 609799
    NPHP4 chr1 5922869 6052533 NM_015102 30 607215
    FRAS1 chr4 78978723 79465423 NM_025074 74 607830
    XDH chr2 31557187 31637611 NM_000379 36 607633
    MKS1 chr17 56282796 56296966 NM_001165927 18 609883
    FAN1 chr15 31196075 31203991 NM_001146096 4 613534
    TCTN2 chr12 124155659 124192950 NM_001143850 18 613846
    NPHS1 chr19 36316273 36342895 NM_004646 29 602716
    CC2D2A chr4 15471488 15603180 NM_001080522 38 612013
    TMEM231 chr16 75572014 75590184 NM_001077416 6 614949
    UPK3A chr22 45680867 45691755 NM_006953 6 611559
    CEP290 chr12 88442789 88535993 NM_025114 54 610142
    NPHP4 chr1 5922869 6052533 NM_015102 30 607215
  • For detection of vision disorders (or the proclivity therefor), the at least one genetic marker is selected from the group consisting of ALMS1, CRB1, CHST6, CRYBA1, PRSS56, GUCY2D, SNRNP200, PDE6C, CNGA3, C8orf37, ABCA4, BBS10, CERKL, GPR125, NHS, LTBP2, GCNT2, RLBP1, MIP, RP1L1, CHM, EYS, TULP1, IGFBP7, CYP1B1, LRAT, MERTK, CNNM4, RP1, RP2, LCA5, MFRP, CNGB1, CACNA1F, KCNV2, CRX, PROM1, TRPM1, PAX6, IMPG2, CDHR1, GPR179, CRYGC, CRYGD, NMNAT1, GALT, ARL6, LRP5, WDR19, SLC4A11, GDF3, SLC16A12, RGS9, RDH12, ADAMS, AIPL1, FAM161A, RPGRIP1, RAB3GAP2, RAB3GAP1, EFEMP1, BEST1, RPE65, EPHA2, FZD4, PRPH2, CRYAA, KCNJ13, NR2E3, BBS9, BBS1, BBS2, BBS5, BBS4, BBS7, SPATA7, CHD7, USH2A, MYO7A, C12orf57, CEP290, NPHP4 and combinations thereof. The details of the vision panel are given below in Table 13.
  • TABLE 13
    Vision Panel
    Number
    of
    Gene Chr Start End Transcript Exons MIM
    ALMS1 chr2 73612885 73837046 NM_015120 23 606844
    CRB1 chr1 197170591 197447585 NM_001257965 15 604210
    CHST6 chr16 75505950 75529282 NM_021615 3 605294
    CRYBA1 chr17 27573874 27581502 NM_005208 6 123610
    PRSS56 chr2 233385172 233390425 NM_001195129 13 613858
    GUCY2D chr17 7905987 7923658 NM_000180 20 600179
    SNRNP200 chr2 96940073 96971307 NM_014014 45 601664
    PDE6C chr10 95372344 95425429 NM_006204 22 600827
    CNGA3 chr2 98962617 99015064 NM_001298 8 600053
    C8orf37 chr8 96257140 96281462 NM_177965 6 614477
    ABCA4 chr1 94458393 94586705 NM_000350 50 601691
    BBS10 chr12 76738265 76742222 NM_024685 2 610148
    CERKL chr2 182401400 182521834 NM_001030311 14 608381
    GPR125 chr4 22388996 22517677 NM_145290 19 612303
    NHS chrX 17653412 17754113 NM_001136024 9 300457
    LTBP2 chr14 74964885 75079034 NM_000428 36 602091
    GCNT2 chr6 10585992 10629601 NM_145655 3 600429
    RLBP1 chr15 89753097 89764922 NM_000326 9 180090
    MIP chr12 56843285 56848435 NM_012064 4 154050
    RP1L1 chr8 10463859 10512617 NM_178857 4 608581
    CHM chrX 85116184 85302566 NM_000390 15 300390
    EYS chr6 64429875 66417118 NM_001142800 43 612424
    TULP1 chr6 35465650 35480647 NM_003322 15 602280
    IGFBP7 chr4 57897236 57976551 NM_001553 5 602867
    CYP1B1 chr2 38294745 38303323 NM_000104 3 601771
    LRAT chr4 155665162 155674270 NM_004744 3 604863
    MERTK chr2 112656190 112786945 NM_006343 19 604705
    CNNM4 chr2 97426638 97477628 NM_020184 7 607805
    RP1 chr8 55528626 55543394 NM_006269 4 603937
    RP2 chrX 46696346 46741791 NM_006915 5 300757
    LCA5 chr6 80194707 80247147 NM_001122769 8 611408
    MFRP chr11 119209643 119217383 NM_015645 15 606227
    CNGB1 chr16 57916243 58005020 NM_001297 33 600724
    CACNA1F chrX 49061522 49089771 NM_001256790 48 300110
    KCNV2 chr9 2717525 2730037 NM_133497 2 607604
    CRX chr19 48325098 48346586 NM_000554 4 602225
    PROM1 chr4 15969848 16077741 NM_006017 27 604365
    TRPM1 chr15 31293263 31393929 NM_001252024 28 603576
    PAX6 chr11 31806339 31833731 NM_001258463 14 607108
    IMPG2 chr3 100941389 101039419 NM_016247 19 607056
    CDHR1 chr10 85954390 85979376 NM_001171971 17 609502
    GPR179 chr17 36481492 36499693 NM_001004334 11 614515
    CRYGC chr2 208992860 208994554 NM_020989 3 123680
    CRYGD chr2 208986330 208989313 NM_006891 3 123690
    NMNAT1 chr1 10003485 10045556 NM_022787 5 608700
    GALT chr9 34646585 34650595 NM_000155 11 606999
    ARL6 chr3 97483364 97520086 NR_103511 10 608845
    LRP5 chr11 68080107 68216743 NM_002335 23 603506
    WDR19 chr4 39184023 39287430 NM_025132 37 608151
    SLC4A11 chr20 3208062 3219887 NM_001174089 20 610206
    GDF3 chr12 7842380 7848360 NM_020634 2 606522
    SLC16A12 chr10 91190050 91295313 NM_213606 8 611910
    RGS9 chr17 63133455 63223821 NM_001081955 19 604067
    RDH12 chr14 68168602 68201168 NM_152443 9 608830
    ADAM9 chr8 38854504 38962779 NM_003816 22 602713
    AIPL1 chr17 6327058 6338519 NM_014336 6 604392
    FAM161A chr2 62051982 62081278 NM_001201543 7 613596
    RPGRIP1 chr14 21756135 21819460 NM_020366 24 605446
    RAB3GAP2 chr1 220321609 220445843 NM_012414 35 609275
    RAB3GAP1 chr2 135809834 135928279 NM_001172435 25 602536
    EFEMP1 chr2 56093096 56151298 NM_001039349 11 601548
    BEST1 chr11 61717355 61731935 NM_004183 11 607854
    RPE65 chr1 68894506 68915642 NM_000329 14 180069
    EPHA2 chr1 16450831 16482582 NM_004431 17 176946
    FZD4 chr11 86656716 86666440 NM_012193 2 604579
    PRPH2 chr6 42664332 42690358 NM_000322 3 179605
    CRYAA chr21 44589140 44592913 NM_000394 3 123580
    KCNJ13 chr2 233631174 233641278 NM_002242 3 603208
    NR2E3 chr15 72102893 72110597 NM_014249 9 604485
    BBS9 chr7 33169151 33645680 NM_198428 23 607968
    BBS1 chr11 66278077 66301098 NM_024649 17 209901
    BBS2 chr16 56518258 56554008 NM_031885 17 606151
    BBS5 chr2 170336005 170363165 NM_152384 12 603650
    BBS4 chr15 72978519 73030817 NR_045565 17 600374
    BBS7 chr4 122748881 122791652 NM_018190 18 607590
    SPATA7 chr14 88851987 88904804 NM_018418 12 609868
    CHD7 chr8 61591323 61780586 NM_017780 38 608892
  • 642 samples with known mutations were used to calculate the analytical sensitivity of the Mendeliome assay. Overall analytical sensitivity was 79% (507/642). One hundred and thirty-five known mutations were missed by the Mendeliome assay, 46% (62/135) of which were due to a design flaw; i.e., the disease gene was not included in the panel appropriate for the disease presentation. If these 62 cases were to be excluded, the overall analytical sensitivity would increase to 87% (507/580). Based on these positive controls (580), sensitivity for single nucleotide variants was found to be 93% (398/428). However, sensitivity for indels was lower at 72% (109/152). As expected for semiconductor-based Ion Torrent sequencing, the bias against indels was not uniform but was largely sequence context-dependent, especially around homopolymer region.
  • In addition to these positive controls, single nucleotide polymorphism (SNP) genotyping arrays were used (Affymetrix Axiom GT1 chip with ˜580,000 SNPs) coming from 21 patients as a second method of testing the analytical sensitivity. The variants detected by SNP arrays were compared to those detected by the next generation sequencing (NGS) technology for each sample. From a total of 3,319 SNPs lying within the target regions of the panels, the resulting SNP sensitivity was about 95%. Interestingly, 30 extra SNPs were identified that were called by the assay but were not called with high confidence on the chip. For analytical specificity, a predetermined quality score of 100 was used (this takes into account strand-bias, homopolymer errors, etc.). Analytical specificity was based on the Sanger validation of 1,078 variants called by the assay. Sanger sequencing confirmed 93% (819/881) of SNVs and 78% (154/197) of indels that met or were higher than that quality score.
  • A total of 2,357 patients representing a very wide range of suspected genetic diseases were tested by the Mendeliome assay (see Table 14 below for the number of patients tested on each panel). Only one panel was chosen per patient based on the most prominent primary clinical feature. The overall clinical sensitivity (i.e., detection of a likely causal variant that is subsequently confirmed by Sanger sequencing) was 43%. Table 14 also summarizes the clinical sensitivity per panel as well as per clinical feature within each panel. As expected, specialties with the highest referral rate were neurology, dysmorphology, pediatric ophthalmology and immunology because of the nonspecificity of the clinical presentation, extreme and genetic heterogeneity, and because a genetic cause is highly suspected for a large fraction of their patient population. In fact, a relatively high yield for the respective panels of 40%, 38%, 52%, and 37% were noted (see Table 14). Specificity of the presentation appeared to bear appreciably on the clinical sensitivity of the assay. For example, with an objective evidence of skeletal dysplasia the sensitivity of the dymorphology/dysplasia panel was 45% as compared to 32% when any degree of dysmorphism was used as the entry point. Similarly, the finding of a specific pattern of neurological abnormality (e.g., muscular dystrophy and neurodegenerative disorders) was associated with a much higher sensitivity as compared with non-syndromic developmental delay/intellectual disability of any degree (56% and 42% vs 11%). Also consistent with this is the finding that retinal dystrophies (almost always Mendelian in etiology) were more likely to have positive hits than the overall performance of the fision panel (65% vs 52%).
  • TABLE 14
    Clinical Sensitivities Per Panel
    Total Overall
    Patients Clinical
    Gene Panel Type Run Sensitivity Selected Subgroup Clinical Sensitivity
    Cardiovascular 243 28% Cardiomyopathy 32%
    Congenital heart disease 10%
    Arrhythmias 31%
    Aneurysms 29%
    Deafness 147 54% Hearing Loss —
    Dermatology 68 62% Nonspecific Dermatological —
    Features
    Dysmorphology- 354 38% Skeletal dysplasia 45%
    Dysplasia Dysmorphism 32%
    Endocrinology 36 61% Pituitary and Thyroid Disorders —
    Gastroenterology 73 29% Persistent Jaundice —
    Hematology 33 24% Aplastic Anemia —
    Inborn errors of 122 59% Metabolic disorders —
    metabolism
    Neurology 524 40% Syndromic DD/ID_Recognizable 47%
    syndromes
    Syndromic DD/ID NYD (not yet 25%
    determined)_Unrecognizable
    syndrome
    Structural Brain 34%
    (Cerebral/Cerebellar/brain stem)
    and spinal
    malformations/anomalies*1
    Non Syndromic DD/ID NYD (not 11%
    yet determined,
    unrecognizable)*2
    Neurodegenerative disorders 42%
    Coordination*3/Movement 69%
    disorders
    Peripheral neuropathy 33%
    Myopathies/Joint abnormalities*4 56%
    PID 196 37% Primary immunodeficiency —
    disorders
    Pulmonology 36 36% Chronic lung infection suspected —
    cystic fibrosis
    Renal 107 57% Glomerular/Tubular Disorders 41%
    Cystic Kidney Disease 63%
    Kidney Malformation 69%
    Vision 418 52% Retinal dystrophy (syndromic, 65%
    non-syndromic, RP, CRD,
    macular dystrophy, FEVR, GFS)
    Cataract (syndromic and non- 34%
    syndromic)
    Aniridia 33%
    Microphthalmia/anophthalmia 30%
    (with and without coloboma)
    Corneal dystrophy (CHED and all 40%
    other subtypes)
    Others 23%
    *1Primary microcephaly cases are included in this group,
    *2Non syndromic cases of Autism/mental disorder and epilepsy are included under this group,
    *3Ataxia cases secondary to cerebellar hypoplasia are included under the structural brain abnormalities group,
    *4Cases with Arthrogryposis Multiplex syndromes are included under myopathies group.
    PID: Primary immunodeficiency,
    DD: developmental delay,
    ID: intellectual disability,
    RP: retinitis pigmentosa,
    CRD: cone-rod dystrophy,
    FEVR: familial exudative vitreoretinopathy,
    GFS: Goldmann-Favre syndrome,
    CHED: corneal hereditary endothelial dystrophy
  • The clinical sensitivity of the Mendeliome assay (43%) is comparable to the ˜25% reported by several large clinical whole exome sequencing (WES) studies. The Mendeliome assay is inherently limited to established disease genes, so it will miss cases caused by large structural variants and mutations in novel genes, although the design is flexible and allows for the addition of newly published disease genes as frequently as needed, e.g. every six months. 213 cases were randomly selected that were negative by the Mendeliome assay, and these were processed using molecular karyotyping. Thirty-five of these were found to have likely pathogenic de novo copy-number variations (CNVs). If these 35 cases are excluded, the clinical sensitivity of the present method would increase slightly to 44%. The remaining 178 were processed using WES, and only 11% (20/178) were found by WES to have a mutation in a known gene that was missed by the Mendeliome assay. Out of these 20 missed cases, the majority (n=14, 70%) were due to a design flaw (i.e., the disease gene was not included in the panel appropriate for the disease presentation) and this can easily be fixed by a spike-in approach.
  • The remaining six cases represent a limitation of the analytical sensitivity of the next-generation sequencing platform used in this study. On the other hand, it should be noted that two patients were included who had had negative diagnostic WES results prior to their enrollment in the Mendeliome assay, and were found to have likely causal mutations by the latter. These cases were missed at the interpretation phase of WES analysis and were solved by the Mendeliome assay, likely because of the smaller number of variants. The much smaller number of variants to be queried by the Mendeliome assay vs. WES also meant a much more rapid clinical interpretation (average 20 min per panel vs. 2-3 hours per WES). This has markedly reduced the cost of interpretation on top of an already appreciable reduction in running cost (24 panel samples were run per chip vs. one WES per chip). The cost is estimated to be $150 per sample with a range of $75-$150 per sample depending on the panel selected. The cost difference is even more dramatic for de novo mutations (n=31) that we identified in this study, because they are typically identifiable by WES only when a trio design is followed. These de novo mutations were identifiable as likely disease-causing heterozygous mutations in relevant Mendelian genes, and their de novo status was confirmed by Sanger sequencing of a single amplicon in both parents. Also relevant to cost reduction is that five couples who lost children with a likely recessive disease were used, but there was no access to DNA from the deceased children. By running the appropriate panel on both parents the method was able to identify the likely causal mutation at a much lower cost than the duo WES design that would have been required to reach the same conclusion.
  • WES is frequently requested after one or more genes deemed relevant to the patient's clinical presentation had been excluded by Sanger sequencing in hopes of identifying a novel genetic cause. However, many WES studies have highlighted the frequent encounter of disease-causing mutations in known genes that would not have been considered good candidates owing to the marked discrepancy between their published phenotype and the clinical presentation of the patient especially for neurological and dysmorphic disorders, which are often very heterogeneous clinically. It has been shown that even in familial cases that are carefully enriched for novel gene discovery by excluding all relevant candidate genes by autozygome analysis, 11% of WES will reveal mutations in known genes missed by the enrichment step because the presentation was very atypical. In fact, in many patients with disease-causing mutations identified by the Mendeliome assay, the presentation was sufficiently different from the published phenotype of the respective gene that WES would have been pursued to establish the diagnosis (see Table 15 below). Some of the most dramatic examples are a de novo EP300 mutation causing microcephalic primordial dwarfism, a homozygous ZNF526 mutation causing a novel Noonan-like phenotype, a homozygous IFT122 mutation causing severe ocular anomalies and unusual appendicular skeletal abnormalities, and a de novo KMT2A mutation causing genital abnormalities in an affected female including absent uterus and vagina with remarkable clitoromegaly (see Table 15).
  • On the other hand, mutations in genes were identified which are typically associated with multisystem disorders in patients with a very limited phenotype, e.g., NPHP4 mutation in a patient with isolated retinal dystrophy instead of Senior-Loken syndrome, and RAB3GAP1 causing isolated cataract instead of Warburg Micro syndrome (Table 15). Finally, it should be noted that the highly surprising finding of a homozygous nonsense mutation in TCOF1 causing severe Treacher-Collins syndrome while the carrier parents are completely normal clinically. Interestingly, this mutation had been missed by direct Sanger sequencing of TCOF1, most likely because the expectation was a heterozygous peak on the sequence chromatogram given the dominant nature of the disease. This is the first instance of a recessive inheritance of TCOF1.
  • TABLE 15
    Atypical Phenotypes
    Observed Phenotype compared to
    published phenotype(s)
    Typical/
    Published Previously
    Gene Mutation Phenotype(s) related reported Atypical
    Name Type Status Origin Type to the case feature(s) feature(s)
    FGFR2 Missense HTZ De DD Craniosynostosis Craniofacial Upper eyelid
    Novo syndromes anomalies coloboma
    Sacrococcygeal
    tail
    Syndactyly
    Neonatal
    teeth (with
    Beare-
    Stevenson
    Cutis Gyrata
    Syndrome)
    Choanalatresia
    Thinning of
    the genu of
    corpus
    callosum (with
    Pfeiffer
    Syndrome)
    HRAS Missense HTZ De DD Costello syndrome Dysmorphic Corneal
    Novo facies haziness
    Multiple joint Tracheomalacia
    dislocations and
    bronchomalacia
    COL2A1 Missense HTZ De DD SpondyloMetaepiphyseal Disproportionate Valvular
    Novo dysplasia short disease (mild
    stature TR, MR)
    Thoracic Acanthosis
    dextroscoliosis nigricans
    Metaphyseal
    dysplasia
    Inguinal
    hernia
    Myopia
    TCOF1 Nonsense HMZ Inherited DD Treacher Collins Underdevelopment Confirmed to
    syndrome 1 zygoma be inherited as
    Choanalatresia AR
    Microtia
    No external
    auditory
    meatus
    Malformed
    ossicles and
    semicircular
    canal
    Iris/optic disc
    coloboma
    BRAF Missense HTZ De DD Cardiofaciocutaneous Hypotonia Coarse face
    Novo syndrome Speech delay similar to
    Costello
    syndrome
    No cardiac
    defects
    Acanthosis
    nigricans
    Deep palmar
    and plantar
    creases
    EP300 Nonsense HTZ De DD Rubinstein-Taybi None Atypical
    Novo syndrome 2 dysmorphic
    facies
    Microcephalic
    primordial
    dwarfism
    NFIX Nonsense HTZ Un- DD Sotos Syndrome type 2 Overgrowth Marfanoid
    known GDD Habitus
    Father Normal bone
    was not age
    tested
    GNS Frame- HMZ Inherited DD Mucopolysaccharidosis Mild coarse Advanced RP
    shift type IIID face
    Mild
    hepatomegaly
    Clear cornea
    Skeletal
    manifestations
    COL11A2 Missense HMZ Inherited DD Otospondylomegaepiphyseal Epiphyseal Hypoplastic
    dysplasia dysplasia optic nerve
    CP Mitral valve
    Deafness prolapse and
    regursitation
    IFT122 Splice HMZ Inherited DD Cranioectodermal Nystagmus Iris and optic
    site dysplasia 1 Metaphyseal nerve coloboma
    dysplasia Microphthalmia
    Duplicated
    thumb and big
    toe
    Post-axial
    polydactyly
    Very short
    tibiae compared
    to fibulae
    ROR2 Missense HMZ Parents DD Robinow syndrome Vertebral Atypical
    not Brachydactyly, type anomalies (in fibrochondroge
    tested B1 Robinow nesis-like
    syndrome) skeletal
    dysplasia
    KMT2A Frame- HTZ De DD Wiedemann-Steiner Dysmorphic Absent uterus
    shift Novo syndrome facies and vagina,
    remarkable
    clitoromegaly
    NSD1 Nonsense HTZ De DD Sotos Syndrome 1 Dysmorphic No overgrowth
    Novo facies
    Thin corpus
    callosum,
    PVL and
    colpocephaly
    on MRI brain
    NPHP4 Missense HMZ Inherited Vision Senior_Loken RP Lack of
    syndrome systemic
    involvement
    (isolate RP)
    CNNM4 Missense HMZ Parents Vision Jalili syndrome LCA, retinal Retinal
    not degeneration coloboma
    tested No dental
    anomalies
    BBS4 Frame- Compound Parents Vision Bardet-Biedl RP Lack of other
    shift HTZ not syndrome 4 features of BBS
    tested (isolated RP)
    RAB3GAP1 Nonsense HMZ Likely Vision Warburg micro Congenital Lack of
    inherited syndrome 1 cataract microcephaly
    and severe
    ocular
    anomalies
    ATRX Nonsense Hemizygous Inherited Vision Mental retardation- Microcephaly RP
    hypotonic facies GDD Optic disc
    syndrome, X-linked White matter coloboma
    changes
    ALMS1 Frame- HMZ Inherited Vision Alstrom syndrome Achromatopsia Lack of other
    shift features of
    Alstrom
    syndrome
    (isolated
    achromatopsia)
    STXBP1 Missense HTZ De Neuro Epileptic Seizures Pigmentary
    Novo encephalopathy, early retinal changes
    infantile, 4
    CDKL5 Nonsense HMZ Inherited Neuro Epileptic GDD Macrocephaly
    encephalopathy, early and overgrowth
    infantile, 2 Facial
    dysmorphism
    similar to Sotos
    syndrome but
    normal bone
    age and
    negative NSD1
    mutation
    No Seizures or
    regression
    No abnormal
    movements
    GTDC2 Missense HMZ Inherited Neuro Muscular dystrophy- None Isolated large
    (POMGNT2) dystroglycanopathy occipital
    (congenital with brain encephalocele
    and eye anomalies, No polydactyly
    type A, 8 Neonatal death
    HSD17B4 Missense HMZ Inherited Neuro D-bifunctional protein Neonatal Normal brain
    deficiency seizures MRI
    No skeletal
    manifestations
    or stippling
    No eye
    findings
    No
    dysmorphism
    ATN1 Missense HTZ De Neuro Dentatorubro- None Early onset
    Novo pallidoluysian atrophy static
    encephalopathy
    Novel
    molecular
    mechanism
    (point mutation)
    KIAA0196 Missense HTZ De Neuro Ritscher-Schinzel Seizures Normal brain
    Novo syndrome Speech delay MRI
    Spastic paraplegia 8, and learning No ataxia or
    AD disability spasticity
    ADRA2B Nonsense HMZ Inherited Neuro Non-syndromic ID None Microcephaly
    (Najmabadi et al, GDD
    2011)
    ZNF526 Missense HMZ Inherited Neuro Mild non-syndromic None Novel Noonan
    ID (Najmabadi et al. like phenotype
    2011) GDD
    WDR45B Nonsense HMZ Inherited Neuro ID and microcephaly Primary Epilepsy
    (WDR45L) (Najmabadi et al, microcephaly White matter
    2011) changes, brain
    atrophy,
    hypoplastic
    corpus callosum
    WDR81 Nonsense HMZ Inherited Neuro Cerebellar Cerebellar Normal corpus
    ataxia, Mental hypoplasia callosum
    retardation, and Prenatal onset
    Dysequilibrium complicated by
    syndrome 2 neonatal death
    (*) Atypical case is defined as a case that has unusual clinical features, unusual mode of inheritance, a novel phenotype or lack of typical features.
    DD: Dysmorphia-Dysplasia Panel,
    GDD: Global Developmental Delay,
    FTT: Failure to Thrive
  • Large scale genomic studies offer opportunities to improve the annotation of the human variome. This study, in which more than 2,300 well phenotyped human patients in a highly consanguineous population have been specifically tested for established disease genes, offered several advantages. First, the study was able to confirm genes that were only considered candidates because their candidacy was based on single mutations/families, so their status based on this study should be upgraded in the Online Mendelian Inheritance in Man (OMIM) database as such (e.g., ARL14EP, ZNF526, WDR45B, and WDR81). Second, the study added 446 novel disease alleles from a total of 795 variants, the largest to be reported in a single study. Third, the very large number of variants identified in the course of this study represented an unprecedented resource on the Arab variome (nearly all patients in this study were Arab in ethnicity), and this will be invaluable to the interpretation of clinical molecular genetic tests on Mendelian genes in Arab patients since it will help address the uncertainty surrounding the identification of many Arab-specific or Arab-enriched variants. Fourth, the high degree of consanguinity allowed the study to observe many variants in homozygosity as a result of autozygosity. This is particularly helpful when these variants were previously reported as disease-causing because observing them in the homozygous state at a relatively high population frequency strongly argues against their purported disease link. Furthermore, the finding of previously reported disease genes that harbor apparently inactivating mutations in the homozygous state at a relatively high frequency and in patients who lack the purported phenotype challenges their listing as disease genes (e.g., CACNA1F, MYH8, and PRX1) although it is acknowledged they have a potential role of such confounding factors as reduced penetrance.
  • The above method was initially limited to genes that were very likely to be disease-causing in a Mendelian context (based on the best available evidence) in order to eliminate the uncertainty surrounding the finding of variants in genes not known to be linked to human diseases. The study mainly included genes whose pathogenicity was supported by the presence of two pathogenic alleles. However, exceptions were made for genes with a single reported mutation but which were further supported by compelling mouse data or positional mapping data. This is important because it must be acknowledged that clinical WGS/WES currently appears to saddle the divide between clinical care and research.
  • If the Mendeliome assay is negative, it may be easier to prepare the patient for the possibility of identifying a novel genetic cause by WGS/WES that requires confirmation in a research setting. Unlike currently available gene panels, the present method seeks to be as inclusive as possible to minimize the challenge of atypical cases. For example, a gene for myopia presenting with ectopia lentis would still be identified because virtually every gene known to present with a prominent eye phenotype was included in the vision panel. In fact, the present analysis showed that only 3% (62/2,357) of cases may have been missed because the gene was not included in the right panel, and even this limitation can be addressed through a spike-in design. Such a broad and inclusive design was particularly helpful in disease categories that are characterized by a very high rate of heterogeneity. In addition to the vision panel, the high rate of atypical cases identified by the dysmorphology/dysplasia, neurology and immunology panels are also noted, although such cases were encountered in nearly all the panels.
  • Patients with various hereditary disorders most often are referred to the medical geneticist either through their primary care provider or through a medical subspecialist who attended to most prominent clinical presentation (i.e., neurological, ophthalmology, skin, renal, hematological, etc.). Therefore, the present symptom/sign based gene panels, collectively known as “The Mendeliome”, were designed in a way that simulates the way these patients present in clinical practice to the respective specialty.
  • Mendelian disorders are defined as hereditary disorders caused by a single autosomal or X-linked gene. The OMIM database, which currently contains about 4,300 monogenic disorders associated with known Molecular defects, represents the most comprehensive source of such information on monogenic disorders. Therefore, it was used as the primary source for gene identification. However, it was manually curated to ensure that only genes with confirmed links to disease are included. It was also supplemented with additional data from PubMed, Genetic Testing Registry (GTR), and gene tests. As such, the above 13 gene panels, which cover the spectrum of pediatric and adult clinical genetic medicine, were constructed. Within each panel, genes were sorted based on the most prominent sign/symptom with which they are most likely to be associated upon presentation to clinical care. This presentation may help the referring clinician, and without requiring sophisticated knowledge about these genes, decide on the appropriateness of genetic testing using these gene panels. Since many genetic disorders are as likely to present to several medical specialties, the present method allows for redundancy between the different panels (average 15%) such that a gene may be present in more than one panel.
  • 3,070 genes covering over 4,000 Mendelian disorders (as annotated by OMIM up to August of 2013) were used as a basis for the design and synthesis of the highly multiplexed gene panels using Ion AmpliSeq Designer software (produced by Life Technologies of California). Tables 1-3 display the list of genes, their corresponding panels, information about the used transcripts, physical positions, and number of exons. From these 3,070 genes, there are 2,826 genes already listed in the genetic testing registry (GTR). Thirteen panels encompassing nearly all of the OMIM genes were defined broadly based upon clinical disciplines with some redundancy in gene content of individual panels. Primer design was based upon generating amplicons with an average length of 200 bp providing 90% minimum coverage of the coding DNA sequence (CDS) and on average 10 bp flanking regions of associated exons. Following this, in silico design coverage was assessed for compliance with design criteria and manual processes applied on a gene by gene basis to ensure adequate coverage and resolve factors such as 3′-SNPs that could impact primer efficiency. Primers for each panel were then synthesized and pooled into two multiplex reactions based upon polymerase chain reaction (PCR) compatibility minimizing likelihood of primer-primer interactions. Following this, synthesis primer pools were tested for coverage, recommended multiplexing and other quality control (QC) metrics to ensure specifications were met. Panels ranged from 96-758 gene with >90% coverage in 97-100% of genes in each panel.
  • Ten nanograms each of all DNA samples were treated to obtain the Ion Proton AmpliSeq library for one of the thirteen gene panels, as appropriate. DNA was amplified with 10-15 amplification cycles. PCR pools for each sample were combined and subjected to primer digestion with a FuPa reagent. Pooled amplicons were then ligated with universal adapters. After purification, libraries were quantitated by qPCR and normalized to 100 pM. Normalized libraries were barcoded (ligated with 24 different Ion Xpress Barcode adapters) and pooled in equal ratios for emulsion PCR (ePCR) on an Ion OneTouch System. Following ePCR, templated Ion Sphere particles were enriched using the Ion OneTouch ES. Both ePCR and enrichment procedures followed the manufacturer's instructions. The template-positive Ion PI Ion Sphere particles were processed for sequencing on the Ion Proton instrument.
  • The data of each run has been analyzed through a multistep pipeline. In the first step of this pipeline, the quality of the reads were verified and regions of the reads with low quality (less than 20) were trimmed out before alignment. The runs with low yield after this quality check were excluded. In the second step, the reads were aligned to the reference hg19 sequence. The observed depth after alignment ranges from 162X (for the neurology panel including 758 genes) to 840X (for the renal panel including 96 genes). In the third step, the aligned reads were processed for variant calling. In the subsequent step, the variants were annotated using public knowledge databases as well as in-house variants databases. The in-house databases include collections of disease-causing variants published by different Saudi teams and aggregation of the variants produced by the samples in this study.
  • In the final step of the pipeline, the non-relevant variants were filtered out based on their functional characteristics and their abundance in the datasets. Variants that are less likely to play a functional role (intronic and synonymous) and variants that were present in population databases (e.g., in the 1000Genome database with MAF>1%) were filtered out. Furthermore, variants that were frequent in the in-house database were also filtered out; a variant with more than 20 occurrences was considered frequent. The cutoff of 20 occurrences was selected on test data to assure 100% sensitivity. An individual base quality of 100 (using Phred-like score) was also selected to exclude low confidence variants. The few remaining variants were then analyzed based on relevance of gene to phenotype, zygosity (when indicated), and SIFT and PolyPhen scores (for missense variants). Table 16 below shows the efficiency of the filtering strategy. Table 16 shows that the subsequent filtering steps lead to a short list of variants to be examined by domain experts. In this table, and as expected, the larger the panel, the larger the list. It is also important to note that more samples included in the in-house database leads to more filtration power and makes the list even shorter. Ultimately, the recognized causal variant was identified as pathogenic or likely pathogenic as defined by the recent American College of Medical Genetics and Genomics (ACMG) guidelines, and the extensive variant data obtained by sequencing thousands of ethnically comparable patients (Saudis) was helpful in applying population frequency as a reliable criterion for pathogenicity in this study.
  • TABLE 16
    Filtering Results Over All Variant Files
    Public SGP
    Functional Pop. Pop. Zy-
    Panel Input Sites DBs DB Quality gosity
    Cardiovascular 746 338 76 26 9 2
    Deafness 828 257 63 50 17 6
    Dermatology 1113 271 71 41 17 5
    Dysmorphology - 1529 369 80 43 15 2
    Dysplasia
    Endocrinology 1129 326 61 42 19 5
    Gastroenterology 362 190 60 20 6 1
    Hematology 1474 324 79 39 18 3
    Inborn Errors of 1955 571 94 54 24 4
    Metabolism
    Neurology 2885 718 158 87 29 4
    PID 633 309 111 22 6 1
    Pulmonology 723 230 74 39 21 3
    Renal 507 132 35 21 7 1
    Vision 906 341 75 51 17 3
    Total (Averages) 1138 337 80 41 16 3
  • Given that the Mendeliome assay is inherently limited to established disease genes and will miss cases caused by large structural variants, 213 eases that are negative by the Mendeliome assay were randomly selected and processed using molecular karyotyping. CytoScan HD arrays were used for the majority of the patients. This array platform contains 2.6 million markers for copy number variation (CNV) detection, of which 750,000 are genotype SNPs and 1.9 million are nonpolymorphic probes, for whole genome coverage. Briefly, 250 ng of genomic DNA was digested with the restriction enzyme NspI and then ligated to an adapter, followed by polymerase chain reaction (PCR) amplification using a single pair of primers that recognized the adapter sequence. The PCR products were run on a 2% Tris-borate-EDTA (TBE) gel to confirm that the majority of products were between 150 and 2,000 bp in length.
  • To obtain a sufficient quantity of PCR product for further analysis, all products from each sample were combined and purified using magnetic beads. The purified PCR products were fragmented using DNase I and visualized on a 4% TBE agarose gel to confirm that the fragment sizes ranged from 25 to 125 bp. The fragmented PCR products were subsequently end-labeled with biotin and hybridized to the array. Arrays were then washed and stained, and then scanned and analyzed. The hidden Markov model was used to determine the copy-number states and their breakpoints. Thresholds of log2 ratio ≧0.58 and ≦−1 were used to categorize altered regions as CNV gains (amplification) and copy-number losses (deletions), respectively.
  • To minimize the detection of false-positive CNVs arising due to inherent microarray noise, only alterations that involved at least 50 consecutive probes and that were at least 500 kb in size were used to categorize altered regions as CNV gains (amplification), whereas those at least 200 kb in size were used to categorize copy-number losses (deletions). The CNVs detected in the patients were then evaluated based on the ACMG standards and guidelines.
  • The genic content in the CNV interval of all the patients who had a molecular karyotype performed was taken into consideration by seeking recent publications to compare breakpoints, phenotypes, and different sizes of CNVs that overlapped. To exclude aberrations representing common benign CNVs, all the identified CNVs were compared with those reported in the Database of Genomic Variants and those reported in the in-house database for individuals who have been classified as normal.
  • De novo CNVs that met the size cutoff of 200 kb for deletions and 500 kb for duplications (based on the laboratory's consideration of the performance characteristics of the assay used) and were not found in either parent were classified as pathogenic. However, this does not eliminate the possibility that pathogenic CNVs exhibiting incomplete penetrance or variable expressivity can be present in an unaffected parent.
  • The remaining 178 were processed using WES. One hundred nanograms of each DNA sample was treated to obtain the Ion Proton AmpliSeq library. Briefly, DNA was amplified in twelve separate wells with 10 amplification cycles. All twelve PCR pools were combined in one well and subjected to primer digestion performing incubation with FuPa reagent. Amplified exome targets were ligated with Ion P1 and Ion Xpress Barcode adapters. Following this, purification libraries were quantified using qPCR. The prepared exome library was further used for emulsion PCR and templated Ion Sphere particles were enriched using Ion OneTouch ES, both procedures following the manufacturer's instructions. The template-positive Ion PI Ion Sphere particles were processed for sequencing on the Ion Proton instrument. Approximately 15-17 Gb of sequence was generated per sequencing run.
  • It is to be understood that the present invention is not limited to the embodiments described above, but encompasses any and all embodiments within the scope of the following claims.

Claims (1)

I claim:
1. A method for diagnosing cardiovascular disease in a patent, comprising the steps of:
obtaining a sample from a patient;
assaying the sample to determine the presence of at least one genetic marker; and
diagnosing the patient with a cardiovascular disease if the at least one genetic marker is detected, wherein the at least one genetic marker is selected from the group consisting of TTR, MYPN, TTN, COL4A3, KCNH2, SMAD4, NOTCH1, ANK2, PKP2, LDB3, MYH6, MYBPC3, SCN5A, MYL3, CACNA1C, DMD, BAG3, EHMT1, DSG2, ABCC9, KCNE2, RYR2, TTN, TTN-AS1, VCL, SOS1, ANKRD1, ACTN2, DSP, FBN1, CHD7 and combinations thereof.
US15/146,867 2015-05-04 2016-05-04 Method of diagnosing patients with conditions caused by mendelian mutation Abandoned US20160326589A1 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
US15/146,867 US20160326589A1 (en) 2015-05-04 2016-05-04 Method of diagnosing patients with conditions caused by mendelian mutation
PCT/US2016/030860 WO2016179331A1 (en) 2015-05-04 2016-05-04 Method of diagnosing patients with conditions caused by mendelian mutations
PCT/US2016/036953 WO2016201272A1 (en) 2015-06-12 2016-06-10 Method of diagnosing patients with conditions caused by mendelian mutations

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201562156872P 2015-05-04 2015-05-04
US15/146,867 US20160326589A1 (en) 2015-05-04 2016-05-04 Method of diagnosing patients with conditions caused by mendelian mutation

Publications (1)

Publication Number Publication Date
US20160326589A1 true US20160326589A1 (en) 2016-11-10

Family

ID=57218353

Family Applications (1)

Application Number Title Priority Date Filing Date
US15/146,867 Abandoned US20160326589A1 (en) 2015-05-04 2016-05-04 Method of diagnosing patients with conditions caused by mendelian mutation

Country Status (2)

Country Link
US (1) US20160326589A1 (en)
WO (1) WO2016179331A1 (en)

Cited By (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20190114389A1 (en) * 2017-08-04 2019-04-18 Billiontoone, Inc. Target-associated molecules for characterization associated with biological targets
CN110624114A (en) * 2018-06-25 2019-12-31 何伟 Application of CRYGD protein
CN115948530A (en) * 2022-08-01 2023-04-11 湖南家辉生物技术有限公司 Pathogenic gene and primer pair of Turner type X-linked syndrome type mental retardation and application thereof

Families Citing this family (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN106399564B (en) * 2016-11-11 2020-09-15 山东省眼科研究所 Application of ERCC8 gene in detection of congenital cataract combined with keratoconus

Family Cites Families (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7629121B2 (en) * 2004-12-17 2009-12-08 Board Of Regents, The University Of Texas System Notch1 variants associated with cardiovascular disease
US20070042426A1 (en) * 2005-01-28 2007-02-22 Kiernan Urban A Biomarkers and assays for myocardial infarction
WO2009075566A1 (en) * 2007-12-12 2009-06-18 Erasmus University Medical Center Rotterdam Biomarkers for cardiovascular disease
WO2012142159A2 (en) * 2011-04-11 2012-10-18 The Brigham And Women's Hospital, Inc Structural mutations in titin cause dilated cardiomyopathy
US20140129179A1 (en) * 2012-11-08 2014-05-08 Datacolor, Inc. System and apparatus for multi channel gloss measurements

Cited By (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20190114389A1 (en) * 2017-08-04 2019-04-18 Billiontoone, Inc. Target-associated molecules for characterization associated with biological targets
US11646100B2 (en) * 2017-08-04 2023-05-09 Billiontoone, Inc. Target-associated molecules for characterization associated with biological targets
US20230268025A1 (en) * 2017-08-04 2023-08-24 Billiontoone, Inc. Target-associated molecules for characterization associated with biological targets
US12176066B2 (en) * 2017-08-04 2024-12-24 Billiontoone, Inc. Target-associated molecules for characterization associated with biological targets
CN110624114A (en) * 2018-06-25 2019-12-31 何伟 Application of CRYGD protein
CN115948530A (en) * 2022-08-01 2023-04-11 湖南家辉生物技术有限公司 Pathogenic gene and primer pair of Turner type X-linked syndrome type mental retardation and application thereof

Also Published As

Publication number Publication date
WO2016179331A1 (en) 2016-11-10

Similar Documents

Publication Publication Date Title
WO2016201272A1 (en) Method of diagnosing patients with conditions caused by mendelian mutations
Zampaglione et al. Copy-number variation contributes 9% of pathogenicity in the inherited retinal degenerations
Saudi Mendeliome Group falkuaya@ kfshrc. edu. sa Comprehensive gene panels provide advantages over clinical exome sequencing for Mendelian diseases
Westland et al. Clinical integration of genome diagnostics for congenital anomalies of the kidney and urinary tract
Inshaw et al. Genetic variants predisposing most strongly to type 1 diabetes diagnosed under age 7 years lie near candidate genes that function in the immune system and in pancreatic β-cells
Gregory et al. Genetics of amyotrophic lateral sclerosis
Sanna-Cherchi et al. Exome-wide association study identifies GREB1L mutations in congenital kidney malformations
US9940434B2 (en) System for genome analysis and genetic disease diagnosis
US20160281166A1 (en) Methods and systems for screening diseases in subjects
Soderquest et al. Genetic variants alter T-bet binding and gene expression in mucosal inflammatory disease
Allen et al. Next generation sequencing of chromosomal rearrangements in patients with split-hand/split-foot malformation provides evidence for DYNC1I1 exonic enhancers of DLX5/6 expression in humans
Smukowski et al. Progress in amyotrophic lateral sclerosis gene discovery: reflecting on classic approaches and leveraging emerging technologies
Soens et al. Leveraging splice‐affecting variant predictors and a minigene validation system to identify Mendelian disease‐causing variants among exon‐captured variants of uncertain significance
US20160326589A1 (en) Method of diagnosing patients with conditions caused by mendelian mutation
Thomas et al. Screening of living kidney donors for genetic diseases using a comprehensive genetic testing strategy
US20180346981A1 (en) Panel-based Genetic Diagnostic Testing for Inherited Eye Diseases
CN105648043A (en) Kit and uses of kit in detection of shortstature related gene
Okazaki et al. Clinical diagnosis of mendelian disorders using a comprehensive gene-targeted panel test for next-generation sequencing
Panneman et al. Cost-effective sequence analysis of 113 genes in 1,192 probands with retinitis pigmentosa and Leber congenital amaurosis
Micheal et al. Variants in the PRPF8 Gene are Associated with Glaucoma
Zernant et al. Rare and common variants in ROM1 and PRPH2 genes trans-modify Stargardt/ABCA4 disease
Abdi et al. Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study
Li et al. De novo mutations contributes approximately 7% of pathogenicity in inherited eye diseases
Tey et al. Computational analysis of functional SNPs in Alzheimer’s disease-associated endocytosis genes
Guo et al. Advantage of whole exome sequencing over allele-specific and targeted segment sequencing in detection of novel TULP1 mutation in Leber congenital amaurosis

Legal Events

Date Code Title Description
STCB Information on status: application discontinuation

Free format text: ABANDONED -- FAILURE TO RESPOND TO AN OFFICE ACTION

点击 这是indexloc提供的php浏览器服务，不要输入任何密码和下载